Hello, A better way may be to navigate directly with this path -
UCSC Home page http://genome.ucsc.edu -> Genomes -> Human Mar. 2006 (hg18) assembly -> Track group = mRNA and EST Tracks, click on track name "Unigene" Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Pete Shepard" <[email protected]> wrote: > From: "Pete Shepard" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Sent: Wednesday, December 2, 2009 12:10:38 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] unigene ids? > > 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
