After using bedtools shuffle a lot with the -excl set on I noticed that the excluding file has the numeric naming convention whereas my input file has the "chr" naming convention. Does someone know if this will cause any problems? I have generated many shuffled files without any errors or warnings and everything seems fine, so I was wondering if someone knows this, before I eventually need to redo everything?
bedtools shuffle -excl doesn't seem to warn about consistent naming convention
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Ok, so I quickly made a run with a small test data that confirmed that -excl only works when we have naming convention, but that it doesn't warn the user about this when we have inconsistent convention. This is pretty worrisome IMO.
(bedtools v2.30.0)