Question: Visualizing BigWig is UCSC genome browser: link not available
2
gravatar for eurioste
11 days ago by
eurioste40
eurioste40 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

ADD COMMENTlink modified 10 days ago • written 11 days ago by eurioste40

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 REPLYlink written 11 days ago by Devon Ryan1.9k

Galaxy main, sorry for not being specific. Thanks.

ADD REPLYlink written 10 days ago by eurioste40
1
gravatar for eurioste
10 days ago by
eurioste40
eurioste40 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 COMMENTlink written 10 days ago by eurioste40
1
gravatar for Jennifer Hillman Jackson
11 days ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink written 11 days ago by Jennifer Hillman Jackson24k

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

ADD REPLYlink written 10 days ago by eurioste40
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