Good Afternoon Rathi:
You can get a 'single coverage' gene track out of the mm9 refGene
table with the following mysql and kent source tree command:
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A mm9 -Ne \
"select
name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds
from
refGene" > mm9.refGene.gp
$ genePredSingleCover mm9.refGene.gp stdout | sort > mm9.refGene.singleCover.gp
See also:
http://genome.ucsc.edu/admin/cvs.html
http://genome.ucsc.edu/admin/jk-install.html
And two scripts and a configuration file that can fetch and
build the source tree:
http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/scripts/kentSrcUpdate.sh
http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/scripts/beta.cvsup.pl
http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/scripts/browserEnvironment.txt
--Hiram
Rathi Thiagarajan wrote:
> Hi there,
>
> Could you please advice me the best way to obtain (mm9) RefSeq canonical
> transcripts genomic intervals? I see that there is a table for UCSC genes
> "knownCanonical", but I was wondering if there was something similar just
> for RefSeq? I could just filter for UCSC genes with linked RefSeq ID's but
> was wondering if there was a better way?
>
> Also is it possible to get a non-redundant set of RefSeq exons while still
> retaining the Gene Name information? I have tried to merge the exon
> genomic intervals within Galaxy, but it doesn't return the gene names.
> Bascially, my goal is to get a RefSeq-based locus information either
> through non-redundant exons or non-redundant whole gene co-ordinates.
>
> Thanking you in advance.
>
> Cheers,
> Rathi
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