diff --git a/modules/callpeak_macs2_atac.bds b/modules/callpeak_macs2_atac.bds index 7910fd3..c8ac1d0 100644 --- a/modules/callpeak_macs2_atac.bds +++ b/modules/callpeak_macs2_atac.bds @@ -81,8 +81,8 @@ string[] macs2_atac( string tag, string smooth_window, string pval_thresh, bool --nomodel --shift -$shiftsize --extsize $smooth_window --broad --keep-dup all $extra_param_macs2 //# Sort by Col8 in descending order and replace long peak names in Column 4 with Peak_ - sys sort -k 8gr,8gr "$prefix"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > $bpeakfile - sys sort -k 14gr,14gr "$prefix"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > $gpeakfile + sys slopBed -i "$prefix"_peaks.broadPeak -g "$chrsz" -b 0 | sort -k 8gr,8gr | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > $bpeakfile + sys slopBed -i "$prefix"_peaks.gappedPeak -g "$chrsz" -b 0 | sort -k 14gr,14gr | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > $gpeakfile sys rm -f "$prefix"_peaks.broadPeak sys rm -f "$prefix"_peaks.gappedPeak @@ -91,7 +91,7 @@ string[] macs2_atac( string tag, string smooth_window, string pval_thresh, bool --nomodel --shift -$shiftsize --extsize $smooth_window -B --SPMR --keep-dup all --call-summits $extra_param_macs2 //# Sort by Col8 in descending order and replace long peak names in Column 4 with Peak_ - sys sort -k 8gr,8gr "$prefix"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > $peakfile + sys slopBed -i "$prefix"_peaks.narrowPeak -g "$chrsz" -b 0 | sort -k 8gr,8gr | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > $peakfile sys rm -f "$prefix"_peaks.narrowPeak sys rm -f "$prefix"_peaks.xls sys rm -f "$prefix"_summits.bed