I want to perform HISAT2 aligment in galaxy using a custom genome. In this case I want to use 3'UTR genome from hg38. I obtain it from Table Browser by generating a custom track with 3'UTR of the hg38 and sending the custom track to Galaxy in fasta format.
When I run HISAT2 in Galaxy, it didn't report any error but, when I check the output file rather than appear the summary of the aligments appears the following:
Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:03 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks I
Then, if I check the aligment in Genome Browser it is completely empty. I guess that the problem is with the reference genome that i'm using. Any advice?
P.S.: Forgot to mention that I tried to follow the protocol to build a custom genome from here: https://galaxyproject.org/learn/custom-genomes/
The only thing that I'm not sure how to do is the point about the chromosome identifiers ("Make sure the chromosome identifiers are a match for other inputs")