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???
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.
Hierarchical Graph FM index (HGFM) for a reference genome plus transcripts