Hi Katrina, The coordinates you refer to are the coordinates of the genes targeted by the probesets, not the actual target sequences of each probeset (defined as the region to which the probesets actually hybridize - typically the 3' end of genes for the U133 arrays). Each probeset only targets a small portion of a gene, which is what I'm interested in. I think I'll have to just do a batch BLAT or BLAST using the target sequences. Thanks for trying to help.
Best, Tim Quoting Katrina Learned <[email protected]>: > Hi Tim, > > The coordinates for the U133 Affymetrix probes can be found in the > affyU133 table. The relevant fields are tName, tStart, and tEnd. > qName is the name of the probes. > > You can use the Table Browser to get all of this information. > > Click on "Tables" in the blue menu bar at the top of the page. > Make these selections: > clade: Mammal > genome: Human > assembly: Mar.2006 > region: genome > group: Expression > track: Affy U133 > table: affyU133 > output format: selected fields from primary and related tables > Click "get output". > Select the following fields (and any others you are interested in > getting the data for): tName, tStart, tEnd and qName. > Click "get output". > > Please don't hesitate to contact the mail list if you require further > assistance. > > Katrina Learned > UCSC Genome Bioinformatics Group > > > > [email protected] wrote: >> Hi, >> >> I am trying to obtain genomic coordinates of the U133 Affymetrix probeset >> target sequences. I contacted Affymetrix and they do not provide genomic >> coordinates of target sequences for the U133 arrays. Is there a custom >> annotation track for these coordinates on the UCSC browser? How >> would I find >> out? >> >> Thanks, >> Tim >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
