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Question: Chromosome Coordinates to Annotation
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gravatar for utkarsh.kapoor
8 months ago by
utkarsh.kapoor • 50
University of Vienna, Austria
utkarsh.kapoor • 50 wrote:

Hello,

If I have specific chromosome coordinates, how do I find out if this region is Exon or Intron or UTR? eg. chr9:7205401-7206719 is within an Intron.

I have a long list and can't do this manually. Any suggestions?

Also, my analysis was performed using GENCODE annotation for Mouse (mm10). Sometimes, the same chromosome coordinates can map to multiple genomic contexts. In this situation, is there a "standard" as to how can be rank the contexts?

Thanks,

Utkarsh
intervals annotation overlap join coordinate • 327 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by utkarsh.kapoor • 50
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The chromosome coordinates that define regions could be compared with the coordinates for features in the reference annotation.

Try the tools in the group Operate on Genomic Intervals. Some will preserve all lines in the original inputs, example: Join the intervals of two datasets side-by-side. Those results can be parsed later to group by features or any other common value with tools like Group or Datamash.

The Galaxy 101 has a simple example of comparing two datasets by coordinate overlap. Slightly different method (as there are a few ways to do this). Review and test some tools out to see which work best with your data/desired result: https://galaxyproject.org/tutorials/g101/

All Galaxy tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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