Question: Igv: Can'T Switch To Hg19
0
gravatar for jobinv
7.2 years ago by
jobinv1.1k
Bergen, Norway
jobinv1.1k wrote:

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 • 3.7k views
ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by jobinv1.1k

are you working behind a firewall ?

ADD REPLYlink written 7.2 years ago by Pierre Lindenbaum130k

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

ADD REPLYlink written 7.2 years ago by jobinv1.1k
2

see "Proxy" in http://www.broadinstitute.org/igv/FAQ .

ADD REPLYlink written 7.2 years ago by Pierre Lindenbaum130k

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...

ADD REPLYlink written 7.2 years ago by jobinv1.1k

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

ADD REPLYlink written 7.2 years ago by jobinv1.1k

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'

ADD REPLYlink written 7.2 years ago by Biomonika (Noolean)3.1k

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!

ADD REPLYlink written 7.2 years ago by jobinv1.1k
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