I made a fasta file combining the genome annotations from 2 organisms(S.cerevisiae and S.Pombe). I want to use this file as a reference to align my RNAseq reads. How do I generate HISAT2 indexes for this file? I read the hisat2 manual and looked at a few blogs online but nothing seems to work. Where do I generate indexes? Is it possible to do it on a computer cluster like ada?
Building HISAT2 index should be simple as
hisat2-build genome.fa index_name. You can find detailed options (if you need them) on the manual page.
That said why are you building a composite index of two species? Does your sample have both genomes in it? Are you looking to separate the reads for the two?