Hi Hiram, Thank you very much for gene track. It's exactly what I wanted!
I am currently trying to get this table into a BED format however noticed that the last two columns actually contains the exonStarts and exonEnds rather than blockSizes and blockStarts (which would be exonStarts). Is the blockSizes information readily available somewhere where I can get access to it? Thanks again for all your help. Cheers, Rathi On Sun, 04 Apr 2010 06:03:03 +1000, Hiram Clawson <[email protected]> wrote: > 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 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
