Using HTSeq-count on a SAM file?

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!

rna-seq

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updated 7.7 years ago by ahmad mousavi

• written 7.7 years ago by iannos •

You usually download one. Which organism?

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written 7.7 years ago by WouterDeCoster

1 answer

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

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written 7.7 years ago by ahmad mousavi

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