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Question: Getting Genome Coordinates for a List of ENSEMBL IDs
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gravatar for virlana.shchuka
2.2 years ago by
virlana.shchuka • 0
virlana.shchuka • 0 wrote:

I need to convert a list of ENSEMBL IDs from an RNA-seq dataset to UCSC mm9 genome coordinates. Any suggestions as to how to go about it?
ensembl identifiers ucsc reference-genome • 1.2k views
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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by virlana.shchuka • 0
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gravatar for Devon Ryan
2.2 years ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

Biomart! That will give you the coordinates of each gene and the associated Ensembl gene ID. If you need UCSC chromosome names then you'll have to convert them after the fact. You can use the "Text reformatting" tool for that. If you need help with that, just post a couple lines from the history item you need to convert and I'll post the appropriate 'AWK Program'.
ADD COMMENT • link written 2.2 years ago by Devon Ryan • 1.9k
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