Hello Sara, For UCSC Genes, the table kgTargetAli has the same alignment information as the refSeqAli table does for the RefSeq Genes track.
Please examine and let us know if this is not what you were looking for. Thanks, Jennifer ps. To learn about the tables/files associated with any track, use the Table browser. http://genome.ucsc.edu/cgi-bin/hgTables Set the clade, genome, assembly, group, and track. Then, next to the default table, use the button "describe table schema". The resulting page will have the default table's schema description and below will be a list of linked tables (with the primary/foreign key links defined). Click on any of these linked tables to bring them up to the "top" to get a full schema description and below a list of that table's linked tables. This is a great way to navigate the data before ftp download. --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/17/10 2:31 PM, Sara Grimm wrote: > Hello. > I need to re-construct the pairwise alignments (transcript vs genome) > for some of your reference sets. Specifically, I'm looking to create an > entry something like this: "NM_001160175.1 > 1-72,73-222,223-340,341-419,420-2067 > chr8:18067618-18067689,18068702-18068851,18074386-18074503,18076920-18076998,18079551-1808198:+" > for a given set of transcripts. For RefSeq, I was able to parse this > information out of refSeqAli.txt. However, I cannot find a > corresponding file for your very nice set of entries in the UCSC Known > Genes track. The knownGene.txt table contains only the genomic > coordinates. Given that the sum of the exon blocks in knownGene.txt > does not always match the sequence length in knownGeneMrna.txt, can you > tell me how to reconstruct the transcript segment coordinates for the > pairwise alignment? > Thanks! > > Sara Grimm, PhD > Lineberger Comprehensive Cancer Center > UNC - Chapel Hill > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
