From 23d6e768c65148ef5b0b5a99b71f49e3a3e78cb4 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Thu, 27 Aug 2020 13:32:12 +1000
Subject: [PATCH] remove merging peak files
---
dunnart/Snakefile | 12 ------------
1 file changed, 12 deletions(-)
diff --git a/dunnart/Snakefile b/dunnart/Snakefile
index f697309..816e9a9 100644
--- a/dunnart/Snakefile
+++ b/dunnart/Snakefile
@@ -606,18 +606,6 @@ rule frip:
# Based on ENCODE `overlap_peaks.py` - recommended for histone marks.
# Need to pool peaks first for each replicate
-rule pool_peaks:
- input:
- mark1 = ["results/macs2/A-2_H3K4me3_vs_A-1_input_macs2_peaks.narrowPeak", "results/macs2/B-2_H3K4me3_vs_B-1_input_macs2_peaks.narrowPeak"],
- mark2 = ["results/macs2/A-3_H3K27ac_vs_A-1_input_macs2_peaks.narrowPeak", "results/macs2/B-3_H3K27ac_vs_B-1_input_macs2_peaks.narrowPeak"]
- output:
- mark1 = "results/macs2/H3K4me3_pooled_macs2_peaks.narrowPeak",
- mark2 = "results/macs2/H3K27ac_pooled_macs2_peaks.narrowPeak"
- run:
- shell("cat {input.mark1} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.mark1}")
- shell("cat {input.mark2} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.mark2}")
-
-
rule overlap_peaks_H3K4me3:
input:
peak1="results/macs2/A-2_H3K4me3_vs_A-1_input_macs2_peaks.narrowPeak",
--
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