Cross-species peak level comparisons

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Last updated: 2022-04-04

Checks: 7 0

Knit directory: chipseq-cross-species/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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Seed: set.seed(20220209)

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Session information: recorded

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File paths: relative

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Repository version: f568c60

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    Untracked:  output/qc/H3K4me3_E13.5_overlap.frip
    Untracked:  output/qc/H3K4me3_E13.5_overlap_downSampled.frip
    Untracked:  output/qc/H3K4me3_E14.5_overlap.frip
    Untracked:  output/qc/H3K4me3_E14.5_overlap_downSampled.frip
    Untracked:  output/qc/H3K4me3_E15.5_overlap.frip
    Untracked:  output/qc/H3K4me3_E15.5_overlap_downSampled.frip
    Untracked:  output/qc/H3K4me3_overlap_default_dunnart_downSampled.frip
    Untracked:  output/qc/H3K4me3_overlap_p0.01_dunnart_downSampled.frip
    Untracked:  output/qc/slurmjob.stderr
    Untracked:  output/qc/slurmjob.stdout
    Untracked:  output/qc/ucsc_alignment/
    Untracked:  output/rnaseq/

Unstaged changes:
    Modified:   analysis/mouse_dunnart_peak_features.Rmd
    Modified:   code/basic_wrapper.slurm
    Modified:   output/qc/A-1_input.PPq30.flagstat.qc
    Modified:   output/qc/A-1_input.dedup.flagstat.qc
    Modified:   output/qc/A-1_input.dupmark.flagstat.qc
    Modified:   output/qc/A-1_input.unfiltered.flagstat.qc
    Modified:   output/qc/A-3_H3K27ac.PPq30.flagstat.qc
    Modified:   output/qc/A-3_H3K27ac.dedup.flagstat.qc
    Modified:   output/qc/A-3_H3K27ac.dupmark.flagstat.qc
    Modified:   output/qc/A-3_H3K27ac.unfiltered.flagstat.qc
    Modified:   output/qc/B-1_input.PPq30.flagstat.qc
    Modified:   output/qc/B-1_input.dedup.flagstat.qc
    Modified:   output/qc/B-1_input.dupmark.flagstat.qc
    Modified:   output/qc/B-1_input.unfiltered.flagstat.qc
    Modified:   output/qc/H3K4me3_overlap_default.frip

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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---

Summary tables

After the tables is all the code to compare peaks between species using liftOver and bedtools. It is a lot of repetitive code that I could revise but it was easiest to track it all this way for now. The summary tables show the number of peaks for the different overlaps.

Number of peaks lifted over with no width filtering

Table. Number of peaks lifted over from dunnart to mouse

enhancer_peaks_smiCraTOmm10	promoter_peak_smiCraTOmm10
916	55

Liftover peak summits from dunnart to mouse

Summary of alignable promoter-associated peaks in the mouse and dunnart

summit_width	number of dunnart peaks	liftOver dunnart to mouse	liftOver mouse to dunnart (reciprocal)	% alignable peaks of total peaks	alignable peaks with ENSEMBL annotations	number of alignable peaks with the same nearest gene call before and after liftOver	% of alignable peaks with the same gene call before and after liftOver
50bp	8510	2647	1446	31.104583	1442	1369	94.93759
100bp	8510	2115	996	24.853114	993	945	95.16616
200bp	8510	1318	526	15.487662	525	504	96.00000
300bp	8510	881	338	10.352526	338	322	95.26627
400bp	8510	603	225	7.085781	227	218	96.03524
500bp	8510	417	161	4.900118	166	157	94.57831

Summary of alignable enhancer-associated peaks in the mouse and dunnart

summit_width	number of dunnart peaks	liftOver dunnart to mouse	liftOver mouse to dunnart (reciprocal)	% alignable peaks of total peaks	alignable peaks with ENSEMBL annotations	number of alignable peaks with the same nearest gene call before and after liftOver	% of alignable peaks with the same gene call before and after liftOver
50bp	35676	10181	6955	28.537392	4313	4301	99.72177
100bp	35676	7664	4954	21.482229	3110	3103	99.77492
200bp	35676	4388	2815	12.299585	1805	1800	99.72299
300bp	35676	2575	1638	7.217737	1029	1028	99.90282
400bp	35676	1649	1079	4.622155	750	750	100.00000
500bp	35676	1144	764	3.206637	608	608	100.00000

Alignable peaks with conserved peak activity

Summary of mouse-dunnart conserved a. high-confidence promoter-associated peaks, and b. enhancer-associated peaks.

Summary of mouse-dunnart conserved enhancer-associated peaks

stage	total dunnart peaks	total dunnart to mouse alignable peaks with annotation	conserved peaks	% conserved peaks of alignable peaks	% conserved peaks of total dunnart peaks
E10.5	35676	4313	292	6.770230	0.8184774
E11.5	35676	4313	32	0.741943	0.0896962
E12.5	35676	4313	162	3.756086	0.4540868
E13.5	35676	4313	238	5.518201	0.6671151
E14.5	35676	4313	183	4.242986	0.5129499
E15.5	35676	4313	210	4.869001	0.5886310

Summary of mouse-dunnart conserved high-confidence promoter-associated peaks

stage	total dunnart peaks	total dunnart to mouse alignable peaks with annotation	conserved peaks	% conserved peaks of alignable peaks	% conserved peaks of total dunnart peaks
E10.5	8510	1442	829	57.48960	9.741481
E11.5	8510	1442	703	48.75173	8.260870
E12.5	8510	1442	653	45.28433	7.673325
E13.5	8510	1442	659	45.70042	7.743831
E14.5	8510	1442	677	46.94868	7.955347
E15.5	8510	1442	654	45.35368	7.685076

LiftOver of peak coordinates between species

All peaks with no peak width filtering

## Load modules
conda activate chip
module load ucsc

## Extract peak coordinates
less output/peaks/dunnart_enhancer_peaks.narrowPeak | awk '{print $1,$2,$3}' > output/peaks/dunnart_enhancer_peaks_coord.bed
less output/filtered_peaks/cluster1_dunnart_promoter_peaks.narrowPeak | awk '{print $1,$2,$3}' > output/filtered_peaks/dunnart_promoter_peaks_coord.bed

## LiftOver peak coordinates from dunnart to mouse
liftOver output/peaks/dunnart_enhancer_peaks_coord.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_smiCraTOmm10.bed output/liftover/dunnart_enhancer_smiCraTOmm10_unmapped.bed
liftOver output/filtered_peaks/dunnart_promoter_peaks_coord.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_smiCraTOmm10.bed output/liftover/dunnart_promoter_smiCraTOmm10_unmapped.bed

LiftOver peak summits

Prepare peak summits and extract peak IDs

## Extract peak IDs
less output/peaks/dunnart_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}' | sort > output/peaks/dunnart_enhancer_peaks_IDs.txt
less output/filtered_peaks/cluster1_dunnart_promoter_peaks.narrowPeak | awk -F '\t' '{print $4}' | sort > output/filtered_peaks/dunnart_promoter_peaks_IDs.txt

less output/peaks/E10.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E10.5_enhancer_peaks_IDs.txt
less  output/peaks/E11.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E11.5_enhancer_peaks_IDs.txt
less  output/peaks/E12.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E12.5_enhancer_peaks_IDs.txt
less  output/peaks/E13.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E13.5_enhancer_peaks_IDs.txt
less  output/peaks/E14.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E14.5_enhancer_peaks_IDs.txt
less  output/peaks/E15.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E15.5_enhancer_peaks_IDs.txt

less  output/filtered_peaks/E10_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}' > output/filtered_peaks/E10.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E11_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E11.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E12_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E12.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E13_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E13.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E14_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E14.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E15_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E15.5_promoter_peaks_IDs.txt

## Concatenate pooled summit peak files 

cat output/peaks/H3K4me3_pooled_macs2_default_summits.bed output/peaks/H3K27ac_pooled_macs2_default_summits.bed > output/peaks/H3K4me3_H3K27ac_dunnart_pooled_default_combinedSummits.bed

cat output/peaks/E10.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E10.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E10.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E11.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E11.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E11.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E12.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E12.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E12.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E13.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E13.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E13.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E14.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E14.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E14.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E15.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E15.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E15.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed

Extract rows from summits file based on enhancer and promoter peak IDs

files =list.files(fullPeak_dir, pattern= "macs2_combinedSummits.bed|default_combinedSummits.bed", full.names=T) # create list of files in directory
files = as.list(files)
summits = lapply(files, function(x) fread(x, header=FALSE, sep="\t", quote = "", na.strings=c("", "NA")))
names(summits) <- c("E10", "E11", "E12", "E13", "E14", "E15", "dunnart")

files2 =list.files(fullPeak_dir, pattern= "peaks_IDs.txt", full.names=T) # create list of files in directory
files3 = list.files(filterPeaks_dir, pattern = "peaks_IDs.txt", full.names=T)
files = append(files2, files3)
filenames <- sub('\\_peaks_IDs.txt$', '', basename(files)) 

files = as.list(files)

peak_IDs = lapply(files, function(x) fread(x, header=FALSE, sep="\t", quote = "", na.strings=c("", "NA")))
names(peak_IDs) <- filenames

filtered <- lapply(summits, function(x) x[x$V4 %in% unlist(as.vector(peak_IDs)),])
filtered <- lapply(filtered, function(x) substr(x$V4, 1, 13))

filtered_bind <- rbindlist(filtered,)
filtered_bind$V4 <- substr(filtered_bind$V4, 1,13)
filtered_split <- split(filtered_bind, by = "V4")

names(filtered_split) <- c("E10.5_enhancer", "E10.5_promoter", 
                           "E11.5_enhancer", "E11.5_promoter",
                           "E12.5_enhancer", "E12.5_promoter",
                           "E13.5_enhancer", "E13.5_promoter",
                           "E14.5_enhancer", "E14.5_promoter",
                           "E15.5_enhancer", "E15.5_promoter",
                           "dunnart_promoter", "dunnart_enhancer")

lapply(names(filtered_split), function(x) write.table(filtered_split[[x]], file=paste0("output/liftover/",x,"_summits", ".bed"), sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE))

Extend the summits 25bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 25 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_50bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 25 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_50bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_50bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_50bpsummits.bed

Extend the summits 50bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 50 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_100bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 50 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_100bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_100bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_100bpsummits.bed

Extend the summits 100bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 100 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_200bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 100 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_200bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_200bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_200bpsummits.bed

Extend the summits 150bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 150 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_300bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 150 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_300bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_300bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_300bpsummits.bed

Extend the summits 200bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 200 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_400bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 200 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_400bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_400bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_400bpsummits.bed

Extend the summits 250bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 250 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_500bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 250 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_500bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_500bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_500bpsummits.bed

LiftOver extended peak summits

LiftOver dunnart peaks to mouse genome

## Enhancer-associated peaks
liftOver output/liftover/dunnart_enhancer_50bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_50bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_50bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_100bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_100bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_100bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_200bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_200bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_200bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_300bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_300bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_300bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_400bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_400bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_400bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_500bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_500bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_500bpsummits_smiCraTOmm10_unmapped.bed

## Promoter-associated peaks
liftOver output/liftover/dunnart_promoter_50bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_50bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_50bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_100bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_100bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_100bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_200bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_200bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_200bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_300bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_300bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_300bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_400bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_400bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_400bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_500bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_500bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_500bpsummits_smiCraTOmm10_unmapped.bed

Lift back to the dunnart genome

## Enhancer-associated peaks
liftOver output/liftover/dunnart_enhancer_50bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_100bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_200bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_300bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_400bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_500bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

## Promoter-associated peaks
liftOver output/liftover/dunnart_promoter_50bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_100bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_200bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_300bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_400bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_500bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

Lift back to mouse genome so that everything is in mouse coordinates

## Enhancer-assocaited peaks
liftOver output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

## Promoter-associated peaks 
liftOver output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

Intersect dunnart CREs with mouse CREs

## Promoter-associated peaks
bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_500bpsummits.bed

## Enhancer-associated peaks
bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

Use window to allow intersections within 50 bps

bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak  > output/liftover/E10.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak  > output/liftover/E11.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak  > output/liftover/E12.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak  > output/liftover/E13.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak  > output/liftover/E14.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak  > output/liftover/E15.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed

bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak  > output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak  > output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak  > output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak  > output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak  > output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak  > output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed

Lift dunnart peaks back over to the dunnart genome

liftOver -bedPlus=4 output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

When you lift over a peak from one species to another, does it always land next to the same gene in both species?

Use annotated peak files for all peaks and compare nearest gene call

Intersect annotation file with peak summits

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_50bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_50bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_50bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_50bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_50bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_50bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_50bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_50bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_50bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_50bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_50bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_50bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_50bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_50bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_50bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_50bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_100bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_100bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_100bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_100bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_100bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_100bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_100bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_100bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_100bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_100bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_100bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_100bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_100bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_100bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_100bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_100bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_200bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_200bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_200bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_200bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_200bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_200bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_200bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_200bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_200bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_200bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_200bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_200bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_200bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_200bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_200bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_200bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_300bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_300bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_300bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_300bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_300bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_300bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_300bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_300bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_300bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_300bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_300bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_300bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_300bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_300bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_300bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_300bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_400bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_400bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_400bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_400bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_400bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_400bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_400bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_400bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_400bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_400bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_400bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_400bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_400bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_400bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_400bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_400bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_500bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_500bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_500bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_500bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_500bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_500bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_500bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_500bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_500bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_500bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_500bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_500bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_500bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_500bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_500bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_500bpsummits_annotation.bed

Liftover dunnart peaks with annotation to mouse

liftOver -bedPlus=4 output/liftover/dunnart_promoter_50bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_50bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_50bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_100bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_100bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_100bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_200bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_200bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_200bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_300bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_300bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_300bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_400bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_400bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_400bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_500bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_500bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_500bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_50bpsummits_annotation_edited.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_50bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_50bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_100bpsummits_annotation_edited.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_100bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_100bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_200bpsummits_annotation_edited.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_200bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_200bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_300bpsummits_annotation_edited.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_300bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_300bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_400bpsummits_annotation_edited.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_400bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_400bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_500bpsummits_annotation_edited.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_500bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_500bpsummits_annotation_smiCraTOmm10_unmapped.bed

Liftover peaks with annotation back to dunnart

liftOver -bedPlus=4 output/liftover/dunnart_promoter_50bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_50bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_50bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_100bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_100bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_100bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_200bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_200bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_200bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_300bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_300bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_300bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_400bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_400bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_400bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_500bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_500bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_500bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_50bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_50bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_50bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_100bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_100bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_100bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_200bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_200bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_200bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_300bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_300bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_300bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_400bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_400bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_400bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_500bpsummits_annotation_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_500bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_500bpsummits_annotation_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

Session information

sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /usr/local/easybuild-2019/easybuild/software/compiler/gcc/10.2.0/openblas/0.3.12/lib/libopenblas_haswellp-r0.3.12.so

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] ChIPseeker_1.30.3      GenomicFeatures_1.46.5 AnnotationDbi_1.56.2  
 [4] Biobase_2.54.0         GenomicRanges_1.46.1   GenomeInfoDb_1.30.1   
 [7] IRanges_2.28.0         S4Vectors_0.32.3       BiocGenerics_0.40.0   
[10] forcats_0.5.1          readr_1.4.0            tidyr_1.1.3           
[13] tibble_3.1.2           ggplot2_3.3.3          tidyverse_1.3.1       
[16] purrr_0.3.4            stringr_1.4.0          dplyr_1.0.8           
[19] knitr_1.33             data.table_1.14.0      workflowr_1.7.0       

loaded via a namespace (and not attached):
  [1] utf8_1.2.1                             
  [2] tidyselect_1.1.1                       
  [3] RSQLite_2.2.7                          
  [4] grid_4.1.0                             
  [5] BiocParallel_1.28.3                    
  [6] scatterpie_0.1.7                       
  [7] munsell_0.5.0                          
  [8] withr_2.4.2                            
  [9] colorspace_2.0-1                       
 [10] GOSemSim_2.20.0                        
 [11] filelock_1.0.2                         
 [12] highr_0.9                              
 [13] rstudioapi_0.13                        
 [14] DOSE_3.20.1                            
 [15] MatrixGenerics_1.6.0                   
 [16] git2r_0.28.0                           
 [17] GenomeInfoDbData_1.2.7                 
 [18] polyclip_1.10-0                        
 [19] bit64_4.0.5                            
 [20] farver_2.1.0                           
 [21] rprojroot_2.0.2                        
 [22] vctrs_0.3.8                            
 [23] treeio_1.18.1                          
 [24] generics_0.1.0                         
 [25] xfun_0.23                              
 [26] BiocFileCache_2.2.1                    
 [27] R6_2.5.0                               
 [28] graphlayouts_0.7.1                     
 [29] bitops_1.0-7                           
 [30] cachem_1.0.5                           
 [31] fgsea_1.20.0                           
 [32] gridGraphics_0.5-1                     
 [33] DelayedArray_0.20.0                    
 [34] assertthat_0.2.1                       
 [35] promises_1.2.0.1                       
 [36] BiocIO_1.4.0                           
 [37] scales_1.1.1                           
 [38] ggraph_2.0.5                           
 [39] enrichplot_1.14.2                      
 [40] gtable_0.3.0                           
 [41] processx_3.5.2                         
 [42] tidygraph_1.2.0                        
 [43] rlang_1.0.2                            
 [44] splines_4.1.0                          
 [45] rtracklayer_1.54.0                     
 [46] lazyeval_0.2.2                         
 [47] broom_0.7.6                            
 [48] yaml_2.2.1                             
 [49] reshape2_1.4.4                         
 [50] modelr_0.1.8                           
 [51] backports_1.2.1                        
 [52] httpuv_1.6.1                           
 [53] qvalue_2.26.0                          
 [54] tools_4.1.0                            
 [55] ggplotify_0.1.0                        
 [56] ellipsis_0.3.2                         
 [57] gplots_3.1.1                           
 [58] jquerylib_0.1.4                        
 [59] RColorBrewer_1.1-2                     
 [60] Rcpp_1.0.8.3                           
 [61] plyr_1.8.6                             
 [62] progress_1.2.2                         
 [63] zlibbioc_1.40.0                        
 [64] RCurl_1.98-1.3                         
 [65] ps_1.6.0                               
 [66] prettyunits_1.1.1                      
 [67] viridis_0.6.2                          
 [68] SummarizedExperiment_1.24.0            
 [69] haven_2.4.1                            
 [70] ggrepel_0.9.1                          
 [71] fs_1.5.0                               
 [72] magrittr_2.0.1                         
 [73] DO.db_2.9                              
 [74] reprex_2.0.0                           
 [75] whisker_0.4                            
 [76] matrixStats_0.61.0                     
 [77] hms_1.1.0                              
 [78] patchwork_1.1.1                        
 [79] evaluate_0.14                          
 [80] XML_3.99-0.6                           
 [81] readxl_1.3.1                           
 [82] gridExtra_2.3                          
 [83] compiler_4.1.0                         
 [84] biomaRt_2.50.3                         
 [85] KernSmooth_2.23-20                     
 [86] crayon_1.4.1                           
 [87] shadowtext_0.1.1                       
 [88] htmltools_0.5.1.1                      
 [89] ggfun_0.0.5                            
 [90] later_1.2.0                            
 [91] aplot_0.1.2                            
 [92] lubridate_1.7.10                       
 [93] DBI_1.1.1                              
 [94] tweenr_1.0.2                           
 [95] dbplyr_2.1.1                           
 [96] MASS_7.3-54                            
 [97] rappdirs_0.3.3                         
 [98] boot_1.3-28                            
 [99] Matrix_1.3-4                           
[100] cli_2.5.0                              
[101] parallel_4.1.0                         
[102] igraph_1.2.6                           
[103] pkgconfig_2.0.3                        
[104] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[105] getPass_0.2-2                          
[106] GenomicAlignments_1.30.0               
[107] xml2_1.3.2                             
[108] ggtree_3.2.1                           
[109] bslib_0.2.5.1                          
[110] XVector_0.34.0                         
[111] rvest_1.0.0                            
[112] yulab.utils_0.0.4                      
[113] callr_3.7.0                            
[114] digest_0.6.27                          
[115] Biostrings_2.62.0                      
[116] rmarkdown_2.8                          
[117] cellranger_1.1.0                       
[118] fastmatch_1.1-0                        
[119] tidytree_0.3.9                         
[120] restfulr_0.0.13                        
[121] curl_4.3.1                             
[122] Rsamtools_2.10.0                       
[123] gtools_3.8.2                           
[124] rjson_0.2.20                           
[125] lifecycle_1.0.1                        
[126] nlme_3.1-152                           
[127] jsonlite_1.7.2                         
[128] viridisLite_0.4.0                      
[129] fansi_0.5.0                            
[130] pillar_1.6.1                           
[131] lattice_0.20-44                        
[132] plotrix_3.8-1                          
[133] KEGGREST_1.34.0                        
[134] fastmap_1.1.0                          
[135] httr_1.4.2                             
[136] GO.db_3.14.0                           
[137] glue_1.4.2                             
[138] png_0.1-7                              
[139] bit_4.0.4                              
[140] ggforce_0.3.3                          
[141] stringi_1.6.2                          
[142] sass_0.4.0                             
[143] blob_1.2.1                             
[144] caTools_1.18.2                         
[145] memoise_2.0.0                          
[146] ape_5.5