From 9d9a54907c0c6152bc410c78805da2a231c82db5 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Thu, 27 Aug 2020 13:31:48 +1000
Subject: [PATCH] merge BAM files for replicates
---
dunnart/Snakefile | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/dunnart/Snakefile b/dunnart/Snakefile
index ddc4a10..597c6ca 100644
--- a/dunnart/Snakefile
+++ b/dunnart/Snakefile
@@ -189,6 +189,20 @@ rule indexBam:
shell:
"samtools index -c {input} {output} 2> {log}"
+rule mergeBAMreplicates:
+ input:
+ H3K4me3 = ["results/bowtie2/A-2_H3K4me3_PPq30.sorted.dedup.bam, results/bowtie2/B-2_H3K4me3_PPq30.sorted.dedup.bam"],
+ H3K27ac = ["results/bowtie2/A-3_H3K27ac_PPq30.sorted.dedup.bam, results/bowtie2/B-3_H3K27ac_PPq30.sorted.dedup.bam"]
+ output:
+ H3K4me3 = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
+ H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam"
+ log:
+ H3K4me3 = "logs/H3K4me3.mergeBAM",
+ H3K27ac = "logs/H3K27ac.mergeBAM"
+ run:
+ shell("samtools merge {output.H3K4me3} {input.H3K4me3} 2> {log.H3K4me3}")
+ shell("samtools merge {output.H3K27ac} {input.H3K427ac} 2> {log.H3K27ac}")
+
# ===============================================================================================
# 4. GENERAL ALIGNMENT QC
# > SAMtools flagstat statistics
--
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