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Question: no bam visualization into IGV
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gravatar for ramon.garcia
3.1 years ago by
ramon.garcia • 0
Spain
ramon.garcia • 0 wrote:

Hi all,

I've done a tophat2 mapping of human RNA-seq expts in usegalaxy.org. After getting the accepted hits bam files, and downloading both bam and bai files, I cannot visualize the mapped reads track in my local IGV. Remote visualization in main UCSC is OK.

I also tried sorting in Galaxy the bam files, downloading both bam and bai, but still don't work in local IGV.

Any help would be very much appreciated.

 

Ramon
visualization igv galaxy bam • 1.1k views
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modified 3.1 years ago • written 3.1 years ago by ramon.garcia • 0
0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The usual way to do this is to launch your local IGV (first, this is important), then use Galaxy dataset link "IGV local" to visualize. Does that work for you?

Best, Jen, Galaxy team
ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for ramon.garcia
3.1 years ago by
ramon.garcia • 0
Spain
ramon.garcia • 0 wrote:

Hi Jen,

Yes, I can visualize bam generated as output from Tophat2 (accepted hits) using the link IGV local. Also, if I download directly to my computer the bam and bai, no problem when opening in IGV local.

Problem is when these files are first exported to my dropbox, and then downloaded. Some chromosomes are corretly visualized, but other chr not.

Any hint?

Many thanks

 

Ramon
ADD COMMENT • link written 3.1 years ago by ramon.garcia • 0
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