Problem opening IGV in Galaxy

Question: Problem opening IGV in Galaxy

3.9 years ago by

blur • 20

European Union

blur • 20 wrote:

Hi,

I am having problems using the IGV option in galaxy.

I have a VCF file with varients, but I cannot open it...

Thank you

igv vcf galaxy • 1.6k views

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modified 3.9 years ago • written 3.9 years ago by blur • 20

Are you using usegalaxy.org?

ADD REPLY • link written 3.9 years ago by Bjoern Gruening ♦ 5.1k

3.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

1. What Galaxy server are you working from? The main Galaxy instance is at http://usegalaxy.org and IGV is functioning as normal as far as I know.

2. What is the assigned reference genome (e.g. "database" attribute)? Is it supported by IGV?

3. Did you create the .vcf dataset in Galaxy or upload it? If uploaded, are you able to perform any other functions on it? Open it in Trackster ("Visualizations" within Galaxy)? Confirming the upload is important.

4. If you are trying to use a local IGV - open that application first, then click on the link.

Thanks - this additional investigation may help you solve the problem, or you can send back more info and we can try to help. You can also look at "Similar posts" at the left side of this window --> to see if any of the prior Q&A helps..

Best, Jen, Galaxy team

ADD COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k

3.9 years ago by

blur • 20

European Union

blur • 20 wrote:

Hi - problem solved! I opened IGV first, now I can see the files.

Thank you!

ADD COMMENT • link written 3.9 years ago by blur • 20

Very glad that worked! This comes up every so often and I usually do not ask this, but if you could accept the answer, it will help others that run into a similar problem going forward. (The title for your question is very clear and easy to find). Thanks! Jen

ADD REPLY • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k

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