Update bgd to bw conversion in callpeak_macs2.bds #5
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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,
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The funciton already has But it was not exported so I modified it to |
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Sorry I didn't notice this line before. Thanks! |
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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=Cfixes 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,