Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
C
ChIP-seq
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container registry
Model registry
Operate
Environments
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
IGR-lab
ChIP-seq
Commits
57b3ece0
Commit
57b3ece0
authored
4 years ago
by
Laura Cook
Browse files
Options
Downloads
Patches
Plain Diff
pool peaks using bedtools merge instead
parent
28bc62ed
Branches
Branches containing commit
No related tags found
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
mouse/Snakefile
+50
-50
50 additions, 50 deletions
mouse/Snakefile
with
50 additions
and
50 deletions
mouse/Snakefile
+
50
−
50
View file @
57b3ece0
...
...
@@ -421,57 +421,57 @@ rule frip:
# Based on ENCODE `overlap_peaks.py` - recommended for histone marks.
# Need to pool peaks first for each replicate
#
rule pool_peaks:
#
input:
#
E10 = expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E11 = expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E12 = expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E13 = expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E14 = expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E15 = expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK)
#
output:
#
E10 = expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E11 = expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E12 = expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E13 = expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E14 = expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E15 = expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK)
#
run:
#
shell("cat {input.E10} > {output.E10}")
#
shell("cat {input.E11} > {output.E11}")
#
shell("cat {input.E12} > {output.E12}")
#
shell("cat {input.E13} > {output.E13}")
#
shell("cat {input.E14} > {output.E14}")
#
shell("cat {input.E15} > {output.E15}")
rule pool_peaks:
input:
E10 = expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E11 = expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E12 = expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E13 = expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E14 = expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E15 = expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK)
output:
E10 = expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E11 = expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E12 = expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E13 = expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E14 = expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E15 = expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK)
run:
shell("cat {input.E10}
| sort -k1,1 -k2,2n - | bedtools merge -i -
> {output.E10}")
shell("cat {input.E11}
| sort -k1,1 -k2,2n - | bedtools merge -i -
> {output.E11}")
shell("cat {input.E12}
| sort -k1,1 -k2,2n - | bedtools merge -i -
> {output.E12}")
shell("cat {input.E13}
| sort -k1,1 -k2,2n - | bedtools merge -i -
> {output.E13}")
shell("cat {input.E14}
| sort -k1,1 -k2,2n - | bedtools merge -i -
> {output.E14}")
shell("cat {input.E15}
| sort -k1,1 -k2,2n - | bedtools merge -i -
> {output.E15}")
#
rule overlap_peaks:
#
input:
#
E10= expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E11= expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E12= expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E13= expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E14= expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E15= expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
#
E10_pooled=expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E11_pooled=expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E12_pooled=expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E13_pooled=expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E14_pooled=expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
E15_pooled=expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
#
output:
#
E10= expand("results/macs2/{mark}_E10.5_overlap.narrowPeak", mark=MARK),
#
E11= expand("results/macs2/{mark}_E11.5_overlap.narrowPeak", mark=MARK),
#
E12= expand("results/macs2/{mark}_E12.5_overlap.narrowPeak", mark=MARK),
#
E13= expand("results/macs2/{mark}_E13.5_overlap.narrowPeak", mark=MARK),
#
E14= expand("results/macs2/{mark}_E14.5_overlap.narrowPeak", mark=MARK),
#
E15= expand("results/macs2/{mark}_E15.5_overlap.narrowPeak", mark=MARK)
#
run:
#
shell("python2.7 scripts/overlap_peaks.py {input.E10} {input.E10_pooled} {output.E10}")
#
shell("python2.7 scripts/overlap_peaks.py {input.E11} {input.E11_pooled} {output.E11}")
#
shell("python2.7 scripts/overlap_peaks.py {input.E12} {input.E12_pooled} {output.E12}")
#
shell("python2.7 scripts/overlap_peaks.py {input.E13} {input.E13_pooled} {output.E13}")
#
shell("python2.7 scripts/overlap_peaks.py {input.E14} {input.E14_pooled} {output.E14}")
#
shell("python2.7 scripts/overlap_peaks.py {input.E15} {input.E15_pooled} {output.E15}")
rule overlap_peaks:
input:
E10= expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E11= expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E12= expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E13= expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E14= expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E15= expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
E10_pooled=expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E11_pooled=expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E12_pooled=expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E13_pooled=expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E14_pooled=expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
E15_pooled=expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
output:
E10= expand("results/macs2/{mark}_E10.5_overlap.narrowPeak", mark=MARK),
E11= expand("results/macs2/{mark}_E11.5_overlap.narrowPeak", mark=MARK),
E12= expand("results/macs2/{mark}_E12.5_overlap.narrowPeak", mark=MARK),
E13= expand("results/macs2/{mark}_E13.5_overlap.narrowPeak", mark=MARK),
E14= expand("results/macs2/{mark}_E14.5_overlap.narrowPeak", mark=MARK),
E15= expand("results/macs2/{mark}_E15.5_overlap.narrowPeak", mark=MARK)
run:
shell("python2.7 scripts/overlap_peaks.py {input.E10} {input.E10_pooled} {output.E10}")
shell("python2.7 scripts/overlap_peaks.py {input.E11} {input.E11_pooled} {output.E11}")
shell("python2.7 scripts/overlap_peaks.py {input.E12} {input.E12_pooled} {output.E12}")
shell("python2.7 scripts/overlap_peaks.py {input.E13} {input.E13_pooled} {output.E13}")
shell("python2.7 scripts/overlap_peaks.py {input.E14} {input.E14_pooled} {output.E14}")
shell("python2.7 scripts/overlap_peaks.py {input.E15} {input.E15_pooled} {output.E15}")
# ===============================================================================================
# 10. Combine all QC into multiqc output
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment
