Please note the table browser exercise in the middle of
this slide presentation:
http://genomewiki.ucsc.edu/index.php/Image:BME230_Winter_2010.ppt
It makes exons and intron custom tracks. Not exactly IGR regions,
but will give you the idea. You could fetch the txStart,txEnd
regions of the refGene track from this mysql command line:
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N \
-e "select chrom,txStart,txEnd from refGene;" hg19
And use that for an intersection to get IGR regions.
You can make whole genome custom tracks from the refGene track.
That should not be an excessive operation to request from
the table browser.
--Hiram
Rongkun Shen wrote:
> Hi,
>
> I am trying to make IGR (intergenic regions) custom track from refGene
> from hg19 according to the approach shown here:
>
> https://lists.soe.ucsc.edu/pipermail/genome/2007-March/013036.html
>
> However, it always ended up with waiting for a long time and with a
> broken downloaded .gz file and failing to get custom track in genome
> browser.
>
> Actually I succeeded in hg18 using this approach - the file size is
> about 230kb in .gz format.
>
> I wonder if there is anything I did wrong.
>
> Thanks,
>
> --Rongkun
>
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
