This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Igv: Can'T Switch To Hg19

I have just now opened Integrated Genome Viewer v. 2.3, and in seeing that the default genome is set to "Human hg18", I decided to click on the dropdown menu, select "More...", click on "Human hg19" and then OK. At this point, it starts loading - but nothing happens. It just keeps loading and loading and loading, until I ultimately close down IGV several hours later.

What might I be doing incorrectly?

igv hg19
• 6,313 views • link
written by jobinv jobinv

Ah, yes, it is on the university network. Might that be the issue? Is there a workaround?

• 0 views • link
written by jobinv jobinv

I performed steps 1 and 2 on the page with hg19.genome instead of hg18.genome, because that is the one that I need. This worked fine, and it downloaded. However, I'm not quite seeing what I should do with the proxy server as per the instructions, but I also don't see why I need this since I already have the file downloaded in this case, nor how to get it loaded into IGV...

• 0 views • link
written by jobinv jobinv

Oh! I got it, had to go to Genomes -> Load Genome from file :)

• 0 views • link
written by jobinv jobinv

When I had problems with loading files in igv, it was due to the memory requirements. So I found location of .jar file by typing 'locate igv.jar' and then executed it again with greater amount of memory 'java -Xmx10000m -jar /usr/share/java/igv.jar'

• 0 views • link
written by Biomonika (Noolean) Biomonika (Noolean)

Thanks for the tip, but other files seem to load just fine. It's just the hg19 that doesn't load at all. I haven't had a chance to attempt the proxy solution that Pierre provided yet though, but I do imagine that the firewall is the problem like he suggests. Thanks anyway!

• 0 views • link
written by jobinv jobinv

0 answers

No answers yet.

Log in to answer this question.

More posts like this