From 04dbfdab3a813446939a5fcde2b280a127795178 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Thu, 27 Aug 2020 13:32:01 +1000
Subject: [PATCH] call peaks on merged BAM files
---
dunnart/Snakefile | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
diff --git a/dunnart/Snakefile b/dunnart/Snakefile
index 597c6ca..f697309 100644
--- a/dunnart/Snakefile
+++ b/dunnart/Snakefile
@@ -525,6 +525,37 @@ rule call_peaks_macs2:
-n {params.name} \
-g 2740338543 2> {log} "
+rule call_peaks_macs2_pooled_replicates:
+ input:
+ H3K4me3 = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
+ H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam",
+ control27ac = "results/bowtie2/B-1_input_PPq30.sorted.dedup.bam",
+ control4me3 = "results/bowtie2/A-1_input_PPq30.sorted.dedup.bam"
+ output:
+ "results/macs2/H3K4me3_pooled_macs2_peaks.xls",
+ "results/macs2/H3K4me3_pooled_macs2_summits.bed",
+ "results/macs2/H3K4me3_pooled_macs2_peaks.narrowPeak",
+ "results/macs2/H3K27ac_pooled_macs2_peaks.xls",
+ "results/macs2/H3K27ac_pooled_macs2_summits.bed",
+ "results/macs2/H3K27ac_pooled_macs2_peaks.narrowPeak"
+ log:
+ H3K4me3 ="logs/H3K4me3_pooled_call_peaks_macs2.log",
+ H3K27ac ="logs/H3K27ac_pooled_call_peaks_macs2.log"
+ params:
+ H3K4me3 = "H3K4me3_pooled_macs2",
+ H3K27ac = "H3K27ac_pooled_macs2"
+ run:
+ shell(" macs2 callpeak -f BAMPE -t {input.H3K4me3} \
+ -c {input.control4me3} --keep-dup all \
+ --outdir results/macs2/ -p 0.01 \
+ -n {params.H3K4me3} \
+ -g 2740338543 2> {log.H3K4me3} ")
+ shell("macs2 callpeak -f BAMPE -t {input.H3K27ac} \
+ -c {input.control27ac} --keep-dup all \
+ --outdir results/macs2/ -p 0.01 \
+ -n {params.H3K27ac} \
+ -g 2740338543 2> {H3K27ac} ")
+
# ===============================================================================================
# 8. Peak QC
# > narrow peak counts
--
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