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Question: Galaxy to IGB trouble shoot
1
gravatar for jpere716
3 months ago by
jpere716 • 10
jpere716 • 10 wrote:

Hey,

I am trying to look at some bed files that I have on galaxy through IGB, but every time that I select this option instead of staying in the selected genome browser of homo sapiens it switches to a custom genome. Any suggestions on why this keeps occurring?

Could it be that the files that I uploaded to galaxy are using the hg19 genome, while the IGB software is using the hg38 genome?

Any help is greatly appreciated.

igb galaxy • 96 views
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modified 3 months ago by Jennifer Hillman Jackson ♦ 25k • written 3 months ago by jpere716 • 10
1
gravatar for Jennifer Hillman Jackson
3 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, the genome assigned in Galaxy as the "database" attribute must be an exact match for the genome loaded into IGB. Most data produced by Galaxy tools will already have the database assigned, but you can also add it in. It must be a match for the content or you will have problems (meaning, don't assign data based on hg38 to hg19 or the reverse). FAQ: https://galaxyproject.org/support/#getting-inputs-right >> How do I find, adjust, and/or correct metadata?

The hg19 aka Homo Sapiens Feb 2009 genome build can be added to your IGB. FAQ: https://wiki.transvar.org/display/igbman/Home >> Reference Genomes

In short:

  • Open IGB
  • Load hg19 into your IGB (it is one of their pre-indexed genomes, but it isn't in the default install)
  • Click on the Galaxy dataset link to IGB to display the data into the correct genome version/build

Thanks! Jen, Galaxy team
ADD COMMENT • link written 3 months ago by Jennifer Hillman Jackson ♦ 25k
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