Question: Bedgraph to bigwig galaxy issue
0
gravatar for onspotproductions
2.3 years ago by
United States
onspotproductions40 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 

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by onspotproductions40
0
gravatar for Jennifer Hillman Jackson
2.3 years ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink modified 2.3 years ago • written 2.3 years ago by Jennifer Hillman Jackson24k
0
gravatar for onspotproductions
2.3 years ago by
United States
onspotproductions40 wrote:

Thank you. I made a mistake in not clicking yes for the treat BAM segments as separate intervals.

ADD COMMENTlink written 2.3 years ago by onspotproductions40

Glad this was resolved!! Jen

ADD REPLYlink written 2.3 years ago by Jennifer Hillman Jackson24k
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