TopHat2 to align RNA with or without annotation file

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2.5 years ago

mario_de_manner ▴ 20

I want to align my RNA reads against the human reference genome with TopHat2 in order to count features with HTseq-count and perform differential expression analysis. In TopHat2, you have the option to specify an annotation file (GTF/GFF).

I am wondering if you should parse an annotation file here, since downstream HTseq-count will also make use of an annotation file? Sould I include the annotation file in both programs? Or only in HTseq-count?

RNAseq GFF GTF TopHat2 • 667 views

ADD COMMENT • link 2.5 years ago by mario_de_manner ▴ 20

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you can provide it in the Tophat2 step but you will for sure need to provide it for the htseq-count step

ADD REPLY • link 2.5 years ago by lieven.sterck 15k

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What is the advantage of providing the annotation file to TopHat2? Is it just a matter of computing time?

ADD REPLY • link 2.5 years ago by mario_de_manner ▴ 20

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