Last updated: 2022-03-29

Checks: 2 0

Knit directory: chipseq-cross-species/

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Repository version: ed6c244

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    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/
    Untracked:  slurmjob.stderr
    Untracked:  slurmjob.stdout

Unstaged changes:
    Modified:   analysis/peak_level_comparisons.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

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Rmd 7c723e0 lecook 2022-02-09 Start workflowr project.

Laura Cook

Workflow and analysis of comparative craniofacial ChIP-seq work in the fat-tailed dunnart and mouse

This project involves a number of analysis for the generation of ChIP-seq data for the fat-tailed dunnart for comparison with the exisiting mouse data in ENCODE.

Data preparation and peak calling