[Genome] fetching sequences

[Rachel Harte]

Hello Ally,
I was a bit hasty in my reply - sorry about that. Define regions will work
for obtaining track annotations in regions that you define. In order to
get sequence, you will need to create a custom track. If you click on the
"Genomes" link on the top blue bar, then you will see a "add custom
tracks" button. Click on this and then select a genome and assembly. You
can load your postions in using BED format.  One you have submitted it,
you will be taken to a Custom Track Manager page. There, if you click on
the "go to table browser" button, you will be able to see and use your
track in the Table Browser. Select "Custom Track" as the group. Select
your custom track. Make sure that "genome" is selected as the region. Then
select sequence as the output. This will give you the sequence for the
regions in your custom track.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Thu, 21 Jun 2007, Eran, Alal wrote:

> Hello,
>
>
>
> What is the best way to get the sequence of multiple regions? (input of
> multiple lines of chr start end)
>
>
>
> Thanks!
>
> Ally
>
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>