I am doing an RNA-seq experiment and I ran HiSAT2 with the mm10 reference genome. Then in order to run htseq-count I downloaded grcm38 gtf file from Ensembl. The only gtf file in the galaxy database is mm9. Also, the htseq-count literature states that UCSC encoded gtf files do not work with htseq because "the gene_id attribute incorrectly contains the same value as the transcript_id attribute". Htseq-count results in all reads counts in the "no features" file. Presumably because I ran HiSAt2 with mm10 and htseq-count with grcm38?
So should I go back and run HiSAT2 with grcm38 reference genome? If so, how do I get the grcm38 hisat2 reference index into Galaxy? I tried to download the grcm38 index from the HiSAT2 webpage and I got a folder with about 10 files "genome.2.ht2, genome.3.ht2" for example. There is also a script in the folder called "make_grcm38.sh". When I run this script in that directory, it returns the error "Could not find hisat2-build in current directory or in PATH".
Is there a way to get a mm10 gtf file from UCSC that is compatible with htseqcount into Galaxy? Thanks!!