[Genome] (no subject)

[Rachel Harte]

Hi Robert,

We do have a program that converst PSL to BED format. You can download our
source code:

http://genome.ucsc.edu/FAQ/FAQlicense#license3

It is free for academic, non-profit and personal use. The program is
called pslToBed ad it is in the dirctory: src/hg/pslToBed/.

Alternatively, if you are using the Table Browser, you could use the PSL
file to create a custom track that is visible in the Table Browser. To
reach the interface for custom tracks, either click on Genomes on the top
blue bar and click on the "add custom tracks" button below the pull down
menus for selecting assemblies or click on the same button below the Genome
Browser image. The documentation for creating custom tracks is here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html

This is a very useful tool as not only can you view the custom track in
the Genome Browser but it also appears as a track and table in the Table
Browser (in the Custom Tracks group). You can use the Table Browser to get
the custom track data in BED format or to use it in queries with our
annotations.

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, 26 Apr 2007, Morell, Robert (NIH/NIDCD) [E] wrote:

> Hi,
>
>
>
> I use the Genome Browser extensively, and make my own BEDfiles for
> annotations. The easiest way for me to get the correct coordinates for a
> bedfile entry is to use BLAT. But the output for BLAT is psl, which must
> then be converted. Can you make bedfile output an option for BLAT?
> (Alternatively,  I would use psl format if that were an option from the
> TABLE Browser so I could incorporate existing annotations into my
> personal annotation files.)
>
>
>
> Robert Morell, PhD
>
> Staff Scientist
>
> Laboratory of Molecular Genetics
>
> National Institute on Deafness and Other Communication Disorders (NIDCD)
>
> National Institutes of Health (NIH)
>
>
>
> 5 Research Ct.
>
> Rockville, MD 20850
>
>
>
> 301-402-4249
>
>
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>