From 03140f12afe17e55e824645ca379b4600e092563 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 28 Aug 2020 14:42:53 +1000
Subject: [PATCH] commented out to fix bug later
---
mouse/Snakefile | 59 +++++++++++++++----------------------------------
1 file changed, 18 insertions(+), 41 deletions(-)
diff --git a/mouse/Snakefile b/mouse/Snakefile
index ac9da71..f0e2d17 100644
--- a/mouse/Snakefile
+++ b/mouse/Snakefile
@@ -554,50 +554,27 @@ 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} | 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),
+ E10= expand(["results/macs2/{case}_vs_{control}_E10.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+ E11= expand(["results/macs2/{case}_vs_{control}_E11.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+ E12= expand(["results/macs2/{case}_vs_{control}_E12.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+ E13= expand(["results/macs2/{case}_vs_{control}_E13.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+ E14= expand(["results/macs2/{case}_vs_{control}_E14.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+ E15= expand(["results/macs2/{case}_vs_{control}_E15.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+ E10_pooled="results/macs2/E10.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+ E11_pooled="results/macs2/E11.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+ E12_pooled="results/macs2/E12.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+ E13_pooled="results/macs2/E13.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+ E14_pooled="results/macs2/E14.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+ E15_pooled="results/macs2/E15.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
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)
+ E10= "results/macs2/H3K27ac_E10.5_overlap.narrowPeak",
+ E11= "results/macs2/H3K27ac_E11.5_overlap.narrowPeak",
+ E12= "results/macs2/H3K27ac_E12.5_overlap.narrowPeak",
+ E13= "results/macs2/H3K27ac_E13.5_overlap.narrowPeak",
+ E14= "results/macs2/H3K27ac_E14.5_overlap.narrowPeak",
+ E15= "results/macs2/H3K27ac_E15.5_overlap.narrowPeak"
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}")
--
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