Difference between revisions of "The Integrative Genomics Viewer"

From QuigleyWiki
Jump to: navigation, search
Line 2: Line 2:
  
  
That's okay, there are lots of other options. Xenbase likes [http://gbrowse.xenbase.org/fgb2/gbrowse/xl8_0/? gBrowse], while I am a real fan of [https://www.broadinstitute.org/igv/ IGV]. So go on down to the site and use it.
+
That's okay, there are lots of other options. Xenbase likes [http://gbrowse.xenbase.org/fgb2/gbrowse/xl8_0/? gBrowse], while I am a real fan of [https://www.broadinstitute.org/igv/ IGV]. So go on down to the site and take it for a spin.
 +
 
 +
 
 +
IGV has two major ways to use it.
 +
 
 +
'''1.''' You can click a button on the site to launch the browser ("Java web start"), which is great for your first time. You can pick a few different options for memory. Depending on what kind of data you're loading, you could get away with a modest option, but if you start loading lots of bams or bedGraphs you're going to run out of memory real quick. Also, if you're using a Mac, Apple Computers is real anal about Java and it's quite possible that your Mac won't want to run Java, even the newest release (turns out Java is a real easy way to sneak into other peoples' computers). So, if that happens, or if you want a little more control over the browser, try the section option.

Revision as of 06:11, 4 July 2015

Genome browsers are great. The UCSC Genome Browser is probably the King of the Browsers (unless you're an Arabidopsis person, in which case it's Annoj), but those guys are a little stuck-up and won't host the X. laevis genome yet. This is a shame, because even the current X. laevis v7b build is way better (n50 of ~3.5 Mb) than lots of genomes already on UCSC (The gorilla n50 is only 1 Mb? Please).


That's okay, there are lots of other options. Xenbase likes gBrowse, while I am a real fan of IGV. So go on down to the site and take it for a spin.


IGV has two major ways to use it.

1. You can click a button on the site to launch the browser ("Java web start"), which is great for your first time. You can pick a few different options for memory. Depending on what kind of data you're loading, you could get away with a modest option, but if you start loading lots of bams or bedGraphs you're going to run out of memory real quick. Also, if you're using a Mac, Apple Computers is real anal about Java and it's quite possible that your Mac won't want to run Java, even the newest release (turns out Java is a real easy way to sneak into other peoples' computers). So, if that happens, or if you want a little more control over the browser, try the section option.