From 2c2a1db7a6ef2a94fefdd63226c1c54cf8b33298 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 28 Aug 2020 14:45:24 +1000
Subject: [PATCH] rule for calculating frip in replicate peaks
---
dunnart/Snakefile | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/dunnart/Snakefile b/dunnart/Snakefile
index 737feb7..1222513 100644
--- a/dunnart/Snakefile
+++ b/dunnart/Snakefile
@@ -636,6 +636,20 @@ rule overlap_peaks_H3K27ac:
shell:
"python2.7 scripts/overlap_peaks.py {input.peak1} {input.peak2} {input.pooled} {output}"
+## Fraction of reads in peaks
+rule overlap_frip:
+ input:
+ H3K4me3bam = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
+ H3K27acbam = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam",
+ H3K4me3bed = "results/macs2/H3K4me3_overlap.narrowPeak",
+ H3K27acbed = "results/macs2/H3K27ac_overlap.narrowPeak"
+ output:
+ H3K4me3frip = "results/qc/H3K4me3_overlap.frip",
+ H3K27acfrip = "results/qc/H3K27ac_overlap.frip"
+ run:
+ shell("python2.7 scripts/encode_frip.py {input.H3K4me3bam} {input.H3K4me3bed} > {output.H3K4me3frip}")
+ shell("python2.7 scripts/encode_frip.py {input.H3K27acbam} {input.H3K27acbed} > {output.H3K27acfrip}")
+
# ===============================================================================================
# 10. Combine all QC into multiqc output
# ===============================================================================================
--
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