Thanks Jennifer,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=uniGene_3 appears to be a dead link, can you resend? Pete On Wed, Dec 2, 2009 at 12:04 PM, Jennifer Jackson <[email protected]> wrote: > Hello, > > You are correct, there is no UniGene track for mouse. The recommended track > for genes is the UCSC Genes track (it combines several input sources and > provides a comprehensive gene summary). However, you can create a Unigene > custom track yourself by using BLAT. > > The general idea is to install BLAT, obtain the query sequences from > UniGene and the genomic sequence from UCSC, then run/filter the output > (perhaps using rules similar to ours, as explained in the human UniGene > track description page, Methods section). > > http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=uniGene_3 > http://genome.ucsc.edu/FAQ/FAQblat > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download > > Once completed, you can use the utility "pslToBed" from the Kent source > tree to create the final BED file. > http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities > http://genome.ucsc.edu/FAQ/FAQdownloads#download27 > > You can load the data as a custom track in PSL or BED format to view your > data versus other annotation if you wish. > > Thanks, > Jennifer > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Pete Shepard" <[email protected]> wrote: > > > From: "Pete Shepard" <[email protected]> > > To: [email protected] > > Sent: Wednesday, December 2, 2009 9:39:11 AM GMT -08:00 US/Canada Pacific > > Subject: [Genome] unigene ids? > > > > Dear Browser, > > > > I am trying to convert unigene ids for mouse, eg "mm.1" , into > > chromome > > locations "bed format". Is there a way to accomplish this using the > > browser? > > > > Also, I am curious as to why there is no unigene track for mouse? Is > > there > > an equivalent track that the browser uses? I know that there is a > > knownIsoform track that clusters genes together, but this track only > > contains ~26,000 clusters and unigene contains ~3x this amount? > > > > Thanks, > > > > Pete > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
