[Genome] trying to extract DNA sequences for introns only

[Kayla Smith]

Hello Sheila,

There are two things going on here which will help you understand your 
results:

1.  The Known Genes track will have items in it that overlap each other. 
  That is, a region that is an exon for one item, may be an intron for 
another item.

2.  When you select "Encode Regions" in the Table Browser, your results 
will include the introns from any Known Gene that overlapped an encode 
region --even if that particular intron does not itself overlap an 
encode region.  In order to get around this problem, you can use the 
Table Browser to do a "basewise" intersection with the encodeRegions table.

Here is a link to a session that I made with 2 custom tracks.  The 
second one, "KGintronsencode_2" is probably what you are looking for:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kayla&hgS_otherUserSessionName=kayla_intron_encode_for_Sheila

If you want to get sequence, go to the Table Browser, select "group: 
Custom Tracks", track: "KGintronsencode_2", output format = "sequence"

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group




Sheila Reynolds wrote:
> I'm trying to extract the DNA sequences for introns only from the Genome
> Browser.  Through the Tables option I tried to ask for the introns only from
> the knownGene track for the ENCODE regions, but if I look at one of the
> regions that is returned (for example chr6:41874646-41971039), it has some
> exons in it (if I am interpreting the genome browser depiction correctly).
> 
> I'd appreciate any tips, I'm rather new at this.
> 
> thanks,
> 
> Sheila Reynolds
> Dept of Electrical Engineering
> University of Washington
> _______________________________________________
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