Question: HISAT2 Output in Galaxy vs Command Line
gravatar for sdbaney
3 months ago by
sdbaney10 wrote:

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?

coordinate sort galaxy bam hisat2 • 111 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by sdbaney10
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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 bam and 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).

For larger BAM outputs, try using curl or wget. How-to is covered in the Galaxy FAQs: > Downloading Data

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k
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