Hello, Ana, I agree that it is not obvious how to get the UTR info from the table downloads, because some of the information is used by multiple assemblies, so it is in the database hgFixed. I will paste some instructions from one of our engineers below that require the use of kent source tree.
However, you can also use the Table Browser to export a BED file that contains fields called thickStart and thickEnd -- references to the display convention of using thick boxes for cds and thin for UTRs, which you refer to. Using the TB, you can use any of the transMapAln* tables and output format, BED - browser extensible data. Here is a link to the format of the extended BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 Here are the details for extracting the info from the tables: hg19 transMapAlnMRna transMapAlnRefSeq transMapAlnUcscGenes hgFixed transMapGeneMRna transMapGeneRefSeq transMapGeneUcscGenes an example: 1. get the PSL, dropping the bin column with cut: hgsql -Ne 'SELECT * FROM transMapAlnRefSeq' hg19 | cut -f 2 > transMapAlnRefSeq.psl 2. get a file containing the CDS hgsql -Ne 'SELECT * FROM transMapGeneRefSeq' hgFixed > transMapGeneRefSeq.cds 3. generate a genePred file, which has UTR annotation mrnaToGene -insertMergeSize=-1 -requireUtr -ignoreUniqSuffix -cdsFile=transMapGeneRefSeq.cds transMapAlnRefSeq.psl transMapGeneRefSeq.gp >&log I hope this helps. regards, --b0b kuhn ucsc genome bioinformatics group On 2/21/2012 1:46 AM, Ana Marques wrote: > Hi all > > How can I get the predicted UTR's and CDSs for transmap gene annotations? > I imagine this is possible because the transmap tracks in the genome browser > have the predicted UTR/CDS annotated. But when the download corresponding > table I only the exons. > > Thank you in advance > > Best Wishes > > Ana Marques > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
