Hello Vishal, You are correct - the human data derived from the HapMap project has been all assigned to the positive strand. The orthologous data for chimp and macaque were generated by UCSC using chain track data and the liftOver program - and this method provided a strand. All of this information is contained within the track description (click on the track name in Assembly browser).
For performing basic unstranded frequency calculations, the simplest option is convert all of the data to the positive strand by complimenting the ortholog SNPs. The reference sequence should not be a concern for this option. Here is a link to some coordinate conversion help: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Vishal R Patel" <[email protected]> wrotes: > From: "Vishal R Patel" <[email protected]> > To: [email protected] > Sent: Thursday, November 19, 2009 4:23:24 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Computing Derived Allele Frequency > > Hi, > > I am trying to compute the Derived Allele Frequency of the SNPs from > HapMap3. Is there an easier way to do it using the > *Database:* hg18 > *Primary Table:* hapmapAllelesChimp > > I am having problems because the reference sequence for Human is on > the > positive strand. While the reference for Chimp is on the positive for > positive strands and negative for strands with negative orientation. > Why is > that? Where is the build information for Chimp data. > > So what is the easiest and fastest way to compute the derived allele > frequency using this table. > > Thank you, > Vishal > -- > Vishal Rajesh Patel > Graduate Student > Universty of California, Irvine > [email protected] > http://www.biognosis.org > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
