From 89deb492613061b8251d13e57d5cd2a8299b1b75 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 28 Aug 2020 14:44:36 +1000
Subject: [PATCH] adding merging of input control BAM files
---
dunnart/Snakefile | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/dunnart/Snakefile b/dunnart/Snakefile
index 446fab2..1a09169 100644
--- a/dunnart/Snakefile
+++ b/dunnart/Snakefile
@@ -198,16 +198,20 @@ rule indexBam:
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"]
+ H3K27ac = ["results/bowtie2/A-3_H3K27ac_PPq30.sorted.dedup.bam", "results/bowtie2/B-3_H3K27ac_PPq30.sorted.dedup.bam"],
+ control = ["results/bowtie2/A-1_input_PPq30.sorted.dedup.bam", "results/bowtie2/B-1_input_PPq30.sorted.dedup.bam"]
output:
H3K4me3 = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
- H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam"
+ H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam",
+ control = "results/bowtie2/input_pooled_PPq30.sorted.dedup.bam"
log:
H3K4me3 = "logs/H3K4me3.mergeBAM",
- H3K27ac = "logs/H3K27ac.mergeBAM"
+ H3K27ac = "logs/H3K27ac.mergeBAM",
+ control = "logs/input.mergeBAM"
run:
shell("samtools merge {output.H3K4me3} {input.H3K4me3} 2> {log.H3K4me3}")
- shell("samtools merge {output.H3K27ac} {input.H3K427ac} 2> {log.H3K27ac}")
+ shell("samtools merge {output.H3K27ac} {input.H3K27ac} 2> {log.H3K27ac}")
+ shell("samtools merge {output.control} {input.control} 2> {log.control}")
# ===============================================================================================
# 4. GENERAL ALIGNMENT QC
--
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