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Question: Visualizing BigWig is UCSC genome browser: link not available
2
gravatar for eurioste
9 months ago by
eurioste • 40
eurioste • 40 wrote:

I wish to visualize some bigwig files generated from bamCoverage tools in the UCSC genome browser (human hg19) but unfortunately I see only the links for "display on IGV/IGB". I did this before but this time the link for the UCSC is missing. Do you know any work around?

EDIT: Sorry for not being clear, I'm using Galaxy main:

I aligned the reads to hg19 with BWA, filtered (Samtools Filter BAM) the low quality mappings and non-canonical contigs and removed duplicates (Samtools RmDup) thus resuting in the BAM file used.

enter image description here
ucsc visualization coverage bam bigwig • 489 views
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modified 9 months ago • written 9 months ago by eurioste • 40

Which Galaxy instance are you using? If you're using the DeepTools2 Galaxy server then this tended not to work, so I think I disabled it (it didn't work due to institute firewall policies).

ADD REPLY • link written 9 months ago by Devon Ryan • 1.9k

Galaxy main, sorry for not being specific. Thanks.

ADD REPLY • link written 9 months ago by eurioste • 40
1
gravatar for eurioste
9 months ago by
eurioste • 40
eurioste • 40 wrote:

Ok, I found out what was missing, I had to edit the dataset attributes and manually add the Database/Build human hg19. This automatically made the UCSC link to appear. Thanks for the answers anyway.
ADD COMMENT • link written 9 months ago by eurioste • 40
1
gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you are working at Galaxy Main https://usegalaxy.org, this functionality is intact. Make sure the database is assigned as hg19 and not one of the other hg19 genome variants (example: hg19female, hg19canon).

Devon commented about the DeepTools2 server. Should you be working at a Galaxy other than these two, contacting the admins of the server is how to find out how they have configured (or disabled) the bigWig > UCSC display functionality.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k

I'm using galaxy main, aligned the reads with BWA to hg19.

ADD REPLY • link written 9 months ago by eurioste • 40
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