From 8e92038c8f3439232a7749ddb12e5ab9b8070507 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 28 Aug 2020 14:42:31 +1000
Subject: [PATCH] call peaks rule for pooled replicates
---
mouse/Snakefile | 61 +++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 61 insertions(+)
diff --git a/mouse/Snakefile b/mouse/Snakefile
index e52ecf1..1b697b3 100644
--- a/mouse/Snakefile
+++ b/mouse/Snakefile
@@ -457,6 +457,67 @@ rule call_peaks_macs2:
-n {params.name} \
-g mm 2> {log} "
+rule call_peaks_macs2_pooled_replicates:
+ input:
+ E10 = "results/bwa/E10.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+ E11 = "results/bwa/E11.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+ E12 = "results/bwa/E12.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+ E13 = "results/bwa/E13.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+ E14 = "results/bwa/E14.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+ E15 = "results/bwa/E15.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+ E10C = "results/bwa/input_E10.5_H3K27ac_q30.sorted.dedup.bam",
+ E11C = "results/bwa/input_E11.5_H3K27ac_q30.sorted.dedup.bam",
+ E12C = "results/bwa/input_E12.5_H3K27ac_q30.sorted.dedup.bam",
+ E13C = "results/bwa/input_E13.5_H3K27ac_q30.sorted.dedup.bam",
+ E14C = "results/bwa/input_E14.5_H3K27ac_q30.sorted.dedup.bam",
+ E15C = "results/bwa/input_E15.5_H3K27ac_q30.sorted.dedup.bam",
+ output:
+ directory("results/macs2/pooled")
+ log:
+ E10 = "results/qc/E10.5_H3K27ac.pooled.macs2",
+ E11 = "results/qc/E11.5_H3K27ac.pooled.macs2",
+ E12 = "results/qc/E12.5_H3K27ac.pooled.macs2",
+ E13 = "results/qc/E13.5_H3K27ac.pooled.macs2",
+ E14 = "results/qc/E14.5_H3K27ac.pooled.macs2",
+ E15 = "results/qc/E15.5_H3K27ac.pooled.macs2",
+ params:
+ E10 = "E10.5_H3K27ac.pooled.macs2",
+ E11 = "E11.5_H3K27ac.pooled.macs2",
+ E12 = "E12.5_H3K27ac.pooled.macs2",
+ E13 = "E13.5_H3K27ac.pooled.macs2",
+ E14 = "E14.5_H3K27ac.pooled.macs2",
+ E15 = "E15.5_H3K27ac.pooled.macs2",
+ run:
+ shell("macs2 callpeak -f BAM -t {input.E10} \
+ -c {input.E10C} --keep-dup all \
+ --outdir results/macs2/ -p 0.01 \
+ -n {params.E10} \
+ -g mm 2> {log.E10}" )
+ shell("macs2 callpeak -f BAM -t {input.E11} \
+ -c {input.E11C} --keep-dup all \
+ --outdir results/macs2/ -p 0.01 \
+ -n {params.E11} \
+ -g mm 2> {log.E11}" )
+ shell("macs2 callpeak -f BAM -t {input.E12} \
+ -c {input.E12C} --keep-dup all \
+ --outdir results/macs2/ -p 0.01 \
+ -n {params.E12} \
+ -g mm 2> {log.E12}" )
+ shell("macs2 callpeak -f BAM -t {input.E13} \
+ -c {input.E13C} --keep-dup all \
+ --outdir results/macs2/ -p 0.01 \
+ -n {params.E13} \
+ -g mm 2> {log.E13}" )
+ shell("macs2 callpeak -f BAM -t {input.E14} \
+ -c {input.E14C} --keep-dup all \
+ --outdir results/macs2/ -p 0.01 \
+ -n {params.E14} \
+ -g mm 2> {log.E14}" )
+ shell("macs2 callpeak -f BAM -t {input.E15} \
+ -c {input.E15C} --keep-dup all \
+ --outdir results/macs2/ -p 0.01 \
+ -n {params.E15} \
+ -g mm 2> {log.E15}" )
# ===============================================================================================
# 8. Peak QC
--
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