From ca31df6fb4f484156eb7c098be3f938158141498 Mon Sep 17 00:00:00 2001 From: florianduclot Date: Wed, 8 Jun 2016 12:09:12 -0400 Subject: [PATCH] Update bgd to bw conversion in callpeak_macs2.bds The bedgraph to BigWig conversion step throws an error on my system for all my files: "(...)pooled.tagAlign.fc.signal.srt.bedgraph is not case-sensitive sorted at line 1879. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again." As mentioned in the error message and at https://gist.github.com/taoliu/2469050, using "LC_COLLATE=C" fixes the issue on my system when the command is ran separately (outside of chipseq.bds pipeline). Would this addition cause conflict with the rest of the code? Thanks, --- modules/callpeak_macs2.bds | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/callpeak_macs2.bds b/modules/callpeak_macs2.bds index 431ed8b..ca6ac26 100644 --- a/modules/callpeak_macs2.bds +++ b/modules/callpeak_macs2.bds @@ -113,7 +113,7 @@ string[] _macs2( string tag, string ctl_tag, string fraglen, bool make_sig, \ slopBed -i "$prefix"_FE.bdg -g $chrsz -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin $chrsz $fc_bedgraph; \ rm -f "$prefix"_FE.bdg; \ \ - sort -k1,1 -k2,2n $fc_bedgraph > $fc_bedgraph_srt; \ + LC_COLLATE=C sort -k1,1 -k2,2n $fc_bedgraph > $fc_bedgraph_srt; \ bedGraphToBigWig $fc_bedgraph_srt $chrsz $fc_bigwig; \ rm -f $fc_bedgraph $fc_bedgraph_srt; \ \ @@ -123,7 +123,7 @@ string[] _macs2( string tag, string ctl_tag, string fraglen, bool make_sig, \ slopBed -i "$prefix"_ppois.bdg -g $chrsz -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin $chrsz $peak_o_dir/$prefix_basename.pval.signal.bedgraph; \ rm -rf "$prefix"_ppois.bdg; \ \ - sort -k1,1 -k2,2n $pval_bedgraph > $pval_bedgraph_srt; \ + LC_COLLATE=C sort -k1,1 -k2,2n $pval_bedgraph > $pval_bedgraph_srt; \ bedGraphToBigWig $pval_bedgraph_srt $chrsz $pval_bigwig; \ \ rm -f $pval_bedgraph $pval_bedgraph_srt; \