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Question: BAM dataset plain text view within Galaxy
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gravatar for bdavenpo65
12 months ago by
bdavenpo65 • 0
bdavenpo65 • 0 wrote:

Viewing Alignment of mRNAseq SRAs to an uploaded cDNA reference genome

I uploaded an SRA accession list from a journal article to Galaxy and used FASTQ Groomer. Then I uploaded a cDNA file to align the SRAs to. I used NGS:Mapping Map with BWA and the each time I try to view one of the four datasets that were mapped, Galaxy stops and it asks if I want to kill the pages. What should I do?

Thanks
convert view sam datatype bam • 434 views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by bdavenpo65 • 0
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I can reproduce the problem where clicking on the "eye" icon to view a BAM dataset within a collection causes the frame to freeze up. Then the browser asks to kill the page. Graphic

Visualizing BAM datasets is new. Before that change, only plain text formats could be viewed and any compressed type would not have a preview.

You can convert to SAM, visualize another way (trackser, genome browser), or maybe use Flatten Collection to access the data outside of a collection.

I am going to run a few tests to figure out if this is a known, how it is reproducible, and the like. If a ticket is created I'll come back and link it in.

Thanks for reporting the problem, Jen, Galaxy team
ADD COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k

Update:

I can only reproduce this when the BAM header is very large. This would be the case for some custom genomes/transcriptomes (tens of thousands of sequences).

Use the tool BAM-to-SAM to convert in cases like this if you want to view the contents of the BAM in plain text. You can extract everything, just the header, or just the result lines.

ADD REPLY • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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