Thank you Maria. Yes, I did explore the Affymetrix csv annotation file yesterday and came to the same conclusion. Having the alignment of the exemplar sequences is helpful in some cases but not specific enough. I will try the UCSC track for probe set alignments. Thanks for the link.
Best wishes, -Christos -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Stalteri, Maria A Sent: Thursday, March 03, 2011 8:17 AM To: [email protected] Subject: [Bioc-sig-seq] 3'-5' position of Affymetrix probe sets Hi, I'm afraid my previous reply was unhelpful, the Affymetrix alignments are for the consensus/exemplar sequences, so would probably give the same genomic coordinates for all the probe sets. The UCSC genome browser has tracks for the genomic alignments of the HG-U133 Plus 2 probes. You can download the underlying data from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/affyU133Plus2.txt.gz or the affyU133Plus2.sql file. Best wishes, Maria _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
