Question: HISAT annotation file?
0
gravatar for zoegward
2.5 years ago by
zoegward60
zoegward60 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 • 1.5k views
ADD COMMENTlink written 2.5 years ago by zoegward60

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 2.5 years ago • written 2.5 years ago by h.mon27k
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