[Genome] Identifying regions in hg17

[Hiram Clawson]

Good Afternoon Jairav:

You can do these types of intersections in the table browser.

Use the table browser to extract from the gene track the different areas
you would like to work with.  Send those results to custom tracks.

Then intersect those custom tracks with your regions which you
have in a custom track.

See also: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

--Hiram

jairav at northwestern.edu wrote:
> Thanks for that, instead of 5 hours, it got that data in 3 minutes! As you can see I'm new to this.
> 
> I have a follow up question:
> 
> -I have a BED file defining > 1000 regions in hg17
> -I would like to identify which regions are in (or partialy in) for example; 1st exon, 1st intron,
> transcription start sites, cds, and a few kb down/up stream.
> 
> I can write a script that takes the output from the tables browser for Known Genes of Gene
> Prediction tracks.  However I had a feeling there would be some better way to do it, as happened earlier.
> 
> Any help would be great.
> 
> Thanks,
> 
> Jairav