Hello Adam, The mRna track does have CDS information defined - and this is what thickStart/thickEnd in BED format represents. No CDS region definition also means no UTR region definition. For cases like this, the data for thickStart/thickEnd will be the same as for chromStart/chromEnd.
For alignment annotation with defined CDS regions, please see tracks in the Gene and Gene Predictions track group such as UCSC Genes and RefSeq Genes. Please note that not all of tracks in this group have both the CDS and the UTRs included in the sequence - read the individual track descriptions for the specifics about any track's contents. http://genome.ucsc.edu/FAQ/FAQformat http://genome.ucsc.edu/FAQ/FAQformat#format1 Please let us know if you need more help, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Adam English" <[email protected]> wrote: > From: "Adam English" <[email protected]> > To: [email protected] > Sent: Thursday, January 21, 2010 11:15:59 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] BED Format Problems > > I'm trying to download all human GRCh37 mRNA in BED format. However, > the > chromStart and chromEnd are always the same as the thickStart and > thickEnd. > What happened to the UTRs? > > -- > Thanks, > ~Adam English > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
