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Question: Genomic Coordinates To Enterz Gene Ids
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gravatar for shamsher jagat
5.5 years ago by
shamsher jagat • 590
United States
shamsher jagat • 590 wrote:
I have a list of around 3000 genomic coordinates of mouse genome and I would iike to extract gene name Enetrz gene ids Is it possible to extract this information in galaxy. Thanks Kanwar
galaxy • 2.4k views
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modified 5.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.5 years ago by shamsher jagat • 590
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gravatar for Jennifer Hillman Jackson
5.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Kanwar, Both UCSC and Biomart have this data. So you could use the tools in "Get Data", pull over the complete set for the genome, then identify overlapping regions versus your coordinates with the tool "Operate on Genomic Intervals -> Join". For UCSC, the track is UCSC Genes (the linked table knownToLocusLink has Entrez ID). For Biomart, you can select the Entrez ID from the list of optional fields to include per species (be sure to avoid any long text description fields or you may get an HTML import error, or test and omit if this comes up). UCSC also has an intersection function in their Table Browser. Send the Galaxy dataset over as a custom track then intersect with the UCSC Genes track. The Table browser's user guide has instructions. Hopefully one of these works out for you! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
ADD COMMENT • link written 5.5 years ago by Jennifer Hillman Jackson ♦ 25k
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