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Question: Bedgraph to bigwig galaxy issue
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gravatar for onspotproductions
3.1 years ago by
onspotproductions • 40
United States
onspotproductions • 40 wrote:

I am attempting to convert a bedgraph coverage map to bigwig for viewing at USCS. However it appears to fill intron regions with unnecessary reads when compared to the original alignment that was done on this data. Any idea why this might be happening?

 

https://www.dropbox.com/s/i1th57hq32us81o/Screen%20Shot%202015-10-28%20at%2012.29.01%20PM.png?dl=0 
conversion galaxy bedgraph bigwig • 1.3k views
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modified 3.1 years ago • written 3.1 years ago by onspotproductions • 40
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gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Just as a guess, the default track settings may be the display problem. Click on the track name to view and adjust.

The tool wrapped for Galaxy is the UCSC version, so the same output should result whether using the utility line-command or within a Galaxy browser (or through the Galaxy API). 

If you need more help with the UCSC Genome Browser, please see: http://genome.ucsc.edu

Thanks, Jen, Galaxy team

 
ADD COMMENT • link modified 3.1 years ago • written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for onspotproductions
3.1 years ago by
onspotproductions • 40
United States
onspotproductions • 40 wrote:

Thank you. I made a mistake in not clicking yes for the treat BAM segments as separate intervals.
ADD COMMENT • link written 3.1 years ago by onspotproductions • 40

Glad this was resolved!! Jen

ADD REPLY • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
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