diff --git a/dunnart/Snakefile b/dunnart/Snakefile index f6973097578ad6a000f3e0dc314ac39db5ec81cb..816e9a9163345ccc13bcddf47055bc9be6ccb81f 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",