[Genome] repeats for refseq genes

[Kayla Smith]

Hello Yael,

You are correct, if you start your intersection with the refGene table,
you wont be able to get the names of the repeats.  And if you start your
intersection with the repeatMasker table, you wont be able to get the
names of the refSeqs.

In order to get the information for both of these tables, you can try
using Galaxy:  http://main.g2.bx.psu.edu/.  Galaxy has more extensie data
intersection tools.  We provide a link in the Table Browser to "send
output to Galaxy"

Here is a previously answered mailing list question with some tips on how
to use Galaxy:
http://www.soe.ucsc.edu/pipermail/genome/2006-November/012256.html

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

Kayla Smith
UCSC Genome Bioinformatics Group

On Mon, 10 Sep 2007, yael shemla wrote:

> Hello,
> I have a list of refseq genes and Im trying to get a list of repeats that
> match each gene.
> If I use the Table of refseq gene with intersection of repeat master table,
> i don't get the names of the repeats.
> If i use the other way, and make intersection of repeat master with
> refseq-table, I cant enter the list of genes.
> Is there another way to get this data?
>
> Thanks.
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