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Question: ChIP-Seq: Galaxy to IGB Visualization
1
gravatar for jasonanthonywhite
11 months ago by
jasonanthonywhite • 20
jasonanthonywhite • 20 wrote:

Hi All,

When trying to view Galaxy generated BAM files (from MACS and/or Star) in IGB, it seems that the database/build associated with the BAM files (hg19 with mtDNA replaced with rCRS) is not recognized by IGB, so the BAM files load in to IGB showing custom genome as oppose to the one identified in Galaxy. I have tried all of the available options in Galaxy to see if any would work but none have been successful. From what I can gather IGB uses UCSC genomes but I am not sure about Galaxy. That seems to leave only two options:

1) Retrieve the fasta file for the Galaxy hg19 genome and use that to create a genome in IGB. However, I have been unable to determine the location of the references.

2) Upload the UCSC genome reference to Galaxy and use that for alignment and MACS, so that I can then visualize in IGB.

Any guidance to solve this issue would be greatly appreciated. Thanks!!
galaxy ibg genome reference chip-seq • 356 views
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modified 11 months ago • written 11 months ago by jasonanthonywhite • 20
1
gravatar for jasonanthonywhite
11 months ago by
jasonanthonywhite • 20
jasonanthonywhite • 20 wrote:

Found the problem. I did not realize that the UCSC genomes were in the database/build drop down menu using different nomenclature than the other assembly sources. I was only looking for genomes that started with "homo sapien" but searching for hg19 or hg38 render additional options. Associating files with hg38 eliminated the transition from Galaxy to IGB problem.
ADD COMMENT • link written 11 months ago by jasonanthonywhite • 20
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