Question: Automatic BAM indexing
gravatar for Sergej.Nowoshilow
28 days ago by
Sergej.Nowoshilow0 wrote:

Dear community,

is there a way to modify the default way Galaxy creates the index *.BAI files? We work with a large salamander genome, therefore, quite some coordinates in the BAM files are beyond 2^30. Therefore, the index files have to be created using either biobambam2:bamSort or samtools index -c -m 14. However, I cannot really figure out if there is a simple way to "teach" Galaxy how to do that. We have our own institute's Galaxy instance, therefore, I can change pretty much anything there...

I am sorry if a similar question was posted before and would be thankful for any advice.

Best regards, Sergej

samtools galaxy bai bam • 68 views
ADD COMMENTlink written 28 days ago by Sergej.Nowoshilow0

Hi - I asked the developers for feedback at the Galaxy Project's Gitter channel here:

Please feel free to comment/or follow up with more info at Gitter if you want. They might reply here or there or ask for more information. I'll check back and link everything together for the final reply/solution.

Thanks! Jen, Galaxy team

ADD REPLYlink written 27 days ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
27 days ago by
United States
Jennifer Hillman Jackson25k wrote:


Even if this was enabled, standard Galaxy tools (from the ToolShed wouldn't be able to use the data as an input. Are you using custom tools, or do you plan to modify tool wrappers to work with this data as well?


Marius van den Beek @mvdbeek 09:49

Yes, we can generate .csi indexes, but I don't think any galaxy tool would be able to do anything with those at the moment.
I assume the issue is mostly that metadata setting doesn't work for that genome ?

Jennifer Hillman-Jackson @jennaj 09:52

Yes, that is how I understand it. They may have custom tools. I pointed the user to this thread, and will prompt them for more info/intended usage.

Plus more now that follows up on tools, alternate formats:

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 26 days ago • written 27 days ago by Jennifer Hillman Jackson25k

Yes, I have a set of custom tools and also adjusted some of the tools from the standard ToolShed. However, I have a feeling that many tools may be just fine if the .csi file is renamed to .bai. Those tools rely on HTS library and, therefore, this naming must be completely transparent for them as the library takes care of the rest. However, I never tested it explicitly. It was just an observation, since a few tools including the IGV browser are just fine with this setup.

ADD REPLYlink written 27 days ago by Sergej.Nowoshilow0
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