Question: Recent problems writing Bigwig from Bam files
1
gravatar for p.barnett
5 months ago by
p.barnett50
p.barnett50 wrote:

I am having problems writing BigWigs using the convert command from an uploaded STAR Bam file. A few weeks ago this wasn't an issue, though had to name sort my Bam file first. Now the file fails, regardless if I sort, don't sort or sort coordinates. Any solutions ?

convert star galaxy bigwig bam • 279 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by p.barnett50
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The function works at Galaxy Main https://usegalaxy.org.

I tested using the "Edit Attributes (pencil icon) > Convert > Convert BAM to Bigwig" function with an RNA STAR produced BAM file that had the database metadata assigned. BAMs are coordinate sorted and include headers when created within Galaxy.

Use SAMTools locally to check that your BAM is intact, has headers, and that the target reference genome used for mapping is the same source/build as the assigned database in Galaxy. Mismatches will cause problems. Upload BAMs with "autodetect datatype" - this can catch/resolve problems (uploaded BAM are sorted and indexed). If a custom genome (genome not hosted at Main), then you'll need to load it to Galaxy, normalize the formatting, promote it to a custom build, then assign that custom database to datasets. https://galaxyproject.org/learn/custom-genomes/#custom-builds

Are you working somewhere else? Or if at Main or can reproduce there, and you cannot solve the problem, this is how to get more help troubleshooting (but please try the above advice first): https://galaxyproject.org/support/#unexpected-results >>

  • My job ended with an error. What can I do?
  • Reporting Usage Issues or Software bugs

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for p.barnett
5 months ago by
p.barnett50
p.barnett50 wrote:

Yes, I'm working on the main galaxy server. I'm guessing the problem lies in the genome I'm using, Rat rn6. I get good mapping on STAR and the features_count function can count it on the main server with no problems using a GTF of rn6. I can also see the BAM file reads if I display it at UCSC...... just cant seem to get a BigWig out of it :-( no matter what I try (though Im probably overlooking something basic). Still need to try uploading and try auto-recognition though... so will give that a try right now

Phil

ADD COMMENTlink modified 5 months ago • written 5 months ago by p.barnett50

I see some successful conversions from around 3 hours ago. Is this worked out now?

If not, which dataset numbers in that larger history present with the problem (reuploaded with autodetect). Please note if you changed the datatype away from what was detected, and why (how did it fail)? Or was the problem content or something else outside of Galaxy?

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for p.barnett
5 months ago by
p.barnett50
p.barnett50 wrote:

OK, fixed my problem. The issue was that the STAR file used for mapping just used chromosome number and not chr(n). So I manually renamed the chromosomes in this file and remapped using STAR. I still need to sort my BAM once I have uploaded it to the Galaxy main, but the BigWig looks fine.

Thanks for reading

Phil

ADD COMMENTlink written 5 months ago by p.barnett50

Ok, good. I didn't see this before I replied above, ignore the comment. Glad you found the problem & solution!

Sometimes just adding "chr" will result in success results (but possibly omitting results) and sometimes complete job failures, it depends on the tool. But you can test that out. If you need help, this FAQ covers a lot of details for troubleshooting/fixing this kind of mismatch, including how to get a copy of the genome build/version indexed at usegalaxy.org: https://galaxyproject.org/support/chrom-identifiers/

ADD REPLYlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 119 users visited in the last hour