[Genome] Question

[Archana Thakkapallayil]

Hello Chen,

This task can be accomplished with the Table Browser intersection tool. 
It will involve first creating a custom track with your BED file. In 
order to get the list of genes that are within 1kb distance to your 
regions, first take the BED file and then subtract 1,000 from all the 
starts and add 1,000 to all the ends (so that all of the chrom regions 
are now 1,000 bases longer on either side). Then upload that BED file as 
a custom track.

Please see the following link for information on creating custom 
annotation tracks:
http://www.genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks

Then intersect your custom track with the 'UCSC Genes' or the 'RefSeq 
Genes' track using the Table Browser intersection tool. More information 
on using the intersection tool is here:
http://www.genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection

Note that when you do a Table Browser intersection, the results only 
give the items and their positions from the first table that you 
selected. So to obtain the list of gene names, you'll have to select the 
gene track as the first track, and your custom track as the second track 
for the intersection.

I hope that this helps. If you have further questions please don't 
hesitate to contact us.

Regards,

Archana
UCSC Genome Bioinformatics Group

Chen Su wrote:
> Hi,
> I have a quick question. I have a BED file with chrom regions. and I'd 
> like to know the list of genes that either overlap or are within 1kb 
> distance to those regions. What's the best way to do this? Thanks a lot 
> for your help!
> - Chen
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>