Question: How To Get Coordinate Information
gravatar for vaibhav jain
7.9 years ago by
vaibhav jain30
vaibhav jain30 wrote:
Hello everyone, I have list of such Id's obtained from  ENSRNOG00000000000 and I want to get the information of the transcription coordinates. So how can I get in Galaxy or can I get it directly from UCSC ??? Vaibhav Jain Research Scholar @IGIB Delhi, INDIA
galaxy • 2.1k views
ADD COMMENTlink modified 7.9 years ago by Jennifer Hillman Jackson25k • written 7.9 years ago by vaibhav jain30
gravatar for Brad Chapman
7.9 years ago by
Brad Chapman240
United States
Brad Chapman240 wrote:
Vaibhav; Those are Ensembl gene identifiers, and the BioMart tool provides a nice web based interface to get coordinates and plenty of other information: Here's an example query to help with getting started: Hope this helps, Brad
ADD COMMENTlink written 7.9 years ago by Brad Chapman240
gravatar for Jennifer Hillman Jackson
7.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Vaibhav, As Brad mentioned, these are Ensembl gene identifiers which would link to at least one, and perhaps more than one, Ensembl transcript. It will be the transcripts that are actually mapped to the genome and that have coordinates. UCSC or Biomart - each of these have methods to input gene identifiers and get out the transcript information (including coordinates). Galaxy can access these through the tool "Get Data". Enter the identifiers into the tools themselves and send result data back into your Galaxy history. When using UCSC, use the track "Ensembl Genes" and paste in the gene name list (up to 1000 at a time). To get a full picture of what is happening in these regions once you have the coordinate intervals of the genomic footprints, the tool "Operate on Genomic Intervals -> Profile Annotations" is highly recommended. This tool will get all sorts of annotation for coordinate regions in one go. Really great for confirming and comparing data between sources and pulling in new information to a project. Hopefully this helps, but if you need more help, please let us know, Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 7.9 years ago by Jennifer Hillman Jackson25k
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