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


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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1890 users visited in the last hour