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Question: Using HTSeq-count on a SAM file?
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I am trying to use HTSeq-count on a SAM file I generated using HISAT2, however it looks like I need a GFF file? How do I generate one of those? Thanks!

ADD COMMENTlink 15 months ago iannos • 0 • updated 15 months ago ahmad mousavi • 430
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You usually download one. Which organism?

ADD REPLYlink 15 months ago
WouterDeCoster
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Hi

For most of known organism you could use Ensemble FTP website it includes DNA sequences and GFF/GTF files. Just search your organism.

ADD COMMENTlink 15 months ago ahmad mousavi • 430

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