[Genome] Conditional Intersections with the GC Percent Track

[Brooke Rhead]

Hello Travis,

Yes, it is possible to do this conditional intersection with the GC 
Percent track.  In the Table Browser, select the GC Percent track first, 
then hit the "filter" button.  Enter "dataValue is > 75%" on the filter 
page.  Hit submit, and then hit the intersection "create" button. 
Choose your custom track on this page, and "All GC Percent records that 
have any overlap with ENCODE Regions".  Hit submit and then choose the 
output type you would like:

BED format (no data value information, only position)
DATA VALUE format (position and real valued data)

or you can choose to make a custom track, which also gives you the two 
options listed above.  Also be sure to choose the "region: genome" radio 
button to include all of the items in your custom track.

I hope this information helps.  Please write back to this list if you 
have further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Travis Ptacek wrote:
> Is it possible to conditionally intersect a custom track (or any 
 > track for that matter) with the GC percent track using the UCSC genome
> browser's table browser? For example, how would I get all of the
 > intervals that intersected with my custom track that had GC
 > percent > 75%?
> 
> If the conditional intersection is not possible, is it possible to
> create a new custom track from the GC percent track that retained the GC
 > percent information (i.e. a list of the 5-mers used in the GC percent
> track, with GC percent incformation, that overlap any given track/custom
> track)?
> 
> Thanks in advance,
> 
> Travis Ptacek
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> Genome maillist  -  Genome at soe.ucsc.edu
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