[Genome] non-redundant set of refseq or knownGenes exons

[Khrebtukova, Irina]

Hi Archana,

my problem is that I do know now how to make a custom track and how to
get a sequence from custom track. I was wondering (and I guess it's now
a FAQ for you guys) how to get NON_REDUNDANT set of exons? Preferably of
course dealing with overlapping exons too. Like selecting largest exon
of all overlapping.

ok, I guess it's still not that easy solution. But my prediction would
be that more and more people would ask this question...

thanks! and of course I just LOVE your browser! really it's the best
despite of my minor desires of making even better.

Irina

-----Original Message-----
From: Archana Thakkapallayil [mailto:archanat at soe.ucsc.edu] 
Sent: Tuesday, August 07, 2007 4:16 PM
To: Khrebtukova, Irina
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] non-redundant set of refseq or knownGenes exons

Hello Irina,

One of my colleagues pointed out to me that you could get this
information by first making a Custom Track using the Table Browser of
all the KnownGene exons. You could then output your custom track in a
BED file and then do some PERL programming to get the unique exons.

1. Creating a custom track of exons.

Set the following options in the Table Browser:
   clade: Vertebrate
   genome: Human
   assembly: Mar 2006
   group: Genes and Gene Prediction Tracks
   track:  UCSC Genes
   table: knownGene
   region: genome
   output format: custom track
   Click "get output". On the next page, select the radio button for 
"Coding Exons" and press "get custom track in table     browser". You 
now have a custom track of the exons of the Known Genes.

2. Back on the Table Browser main page, now choose "Custom Tracks" as
the group and the corresponding track and table. Then choose 'output
format: BED' and hit 'get output'. On this page select the radio button
for 'Create one BED record per: Whole Gene" and press "get BED". This
gives you the coordinates of all the coding exons in the BED format. 
More information on using the Table Browser is here:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

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

Regards,

Archana
UCSC Genome Bioinformatics Group


Khrebtukova, Irina wrote:
> Is there an easy way to get non-redundant set of all refseq and/or 
> knownGenes exons? I mean if the same exon is shared by two or more 
> transcripts it is redundant.
>
> I think this or similar question was already asked. Just can not find 
> the answer.
>
> thanks!
>
> Irina Khrebtukova, PhD
> Sr. Staff Bioinformatics Scientist
> Illumina Inc.
> 25861 Industrial Blvd.,
> Hayward, CA 94545
> ph: 510-723-9219
> ikhrebtukova at illumina.com
>  
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu 
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>