Question: Getting Genome Coordinates for a List of ENSEMBL IDs
gravatar for virlana.shchuka
18 months ago by
virlana.shchuka0 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?

ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson24k • written 18 months ago by virlana.shchuka0
gravatar for Devon Ryan
18 months ago by
Devon Ryan1.9k
Devon Ryan1.9k 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 COMMENTlink written 18 months ago by Devon Ryan1.9k
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