Question: HISAT annotation file?
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gravatar for zoegward
23 months ago by
zoegward50
zoegward50 wrote:

Hi,

I'm trying to use HISAT2 to align my rna-seq reads to. Can anyone clarify whether the genome_tran index files that are available to download from the HISAT2 website have been generated with annotation files???

rna-seq • 1.3k views
ADD COMMENTlink written 23 months ago by zoegward50

Having in mind that genome_tran is a Hierarchical Graph FM index (HGFM) for a reference genome plus transcripts, then yes, it should have been generated with annotations - more specifically, exons taken from a gtf annotation. See the HISAT2 manual for more information.

ADD REPLYlink modified 23 months ago • written 23 months ago by h.mon24k
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