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hartleys / QoRTs

Quality of RNA-Seq Toolset
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Question regarding a few gff files #9

Closed sahilseth closed 8 years ago

sahilseth commented 8 years ago

I see a few files in the example walk-though, was wondering the source for them; and also how were they generated.

Thanks!

sahilseth commented 8 years ago

found the script, step6A.makeFlatAnnoFiles.sh

hartleys commented 8 years ago

forJunctionSeq.gff and forDexSeq.gff are produced by the java jar command: makeFlatGff ( found here: http://hartleys.github.io/QoRTs/jarHtml/makeFlatGff.html ). The dexseq version requires the --DEXSeqFmt option.

withNovel.forJunctionSeq.gff and orphanSplices.gff are generated by the mergeNovelSplices command ( see here: http://hartleys.github.io/QoRTs/jarHtml/mergeNovelSplices.html )

Make sure you are using the most recent version of QoRTs. On Nov 15, 2015 5:21 PM, "sseth" notifications@github.com wrote:

I see a few files in the example walk-though, was wondering the source for them; and also how were they generated.

  • forJunctionSeq.gff.gz
  • forDEXSeq.gff.gz
  • withNovel.forJunctionSeq.gff.gz
  • orphanSplices.gff.gz

Thanks!

— Reply to this email directly or view it on GitHub https://github.com/hartleys/QoRTs/issues/9.