#19 DefinedRegionDifferentialSeq: Would be nice to get an error message if a ".gff" file is supplied

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nobody
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1
2012-12-04
2012-12-04
Alex Williams
No

DefinedRegionDifferentialSeq requires a "refflat" format gene annotation file---it specifically does NOT accept a gff or gtf file, as far as I am aware.

It might be nice if the program could check the filename of the "Refflat" file, and if it sees that it ends in "gtf" or "gff" or "gff3", output an error messaage like: "DefinedRegionDifferentialSeq requires a REFFLAT gene annotation file. You can download one of these for most species, or convert a gff file to refflat using the UCSC Genome Browser tool 'gff3ToGenePred'. Note that gff3ToGenePred is by an external group, and the USEQ authors are unfortunately NOT able to provide usage help or support for it."

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