In galaxy, I am given a BAM and BAI file. Does galaxy implement the sorting and index function that I would need to run through SAMtools if ran from the command line? Or does the galaxy HISAT2 output BAM file need to then be sorted and indexed with SAMtools for use in StringTie?
The Galaxy HISAT2 wrapper coordinate sorts the BAM output.
You should be able to both use that output with other Galaxy wrapped tools or download both the
bai for use with other tools (command-line, browsers, etc).
If for some reason a command-line tool does complain about BAM sorting (perhaps from some older mapper of Galaxy version), then yes, you should try re-sorting line command with SAMtools to see if that resolves the issue as the first pass solution (would be unexpected, but the quickest way forward).
Thanks! Jen, Galaxy team