Hi Ravi, For each human SNPs track, we build a table of orthologous reference alleles in chimp, orangutan and Rhesus macaque. For SNPs (132), the table is snp132OrthoPt2Pa2Rm2 (panTro2, ponAbe2, rheMac2). There is not a standalone assembly for Neandertal, and the Neandertal genome is only partly covered. One of our developers suggests the following using the Table Browser and Galaxy:
1. In the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), make the following selections: clade: Mammal genome: Human assembly: hg19 group: Variation and Repeats track: Common SNPs(132) table: All SNPs(132) intersection: click 'create' then set group: Neandertal Assembly and Analysis, track: S SNPs, table: S SNPs (ntSssSnps), click 'submit' output format: select "Send output to Galaxy" 2. If Galaxy doesn't already have S SNPs, use the Table Browser to send that track to Galaxy. 3. Use Galaxy to do the type of intersection that keeps IDs & other info from both tracks. That will associate SNP IDs with coded alleles in the name field of ntSssSnps -- see track description for S SNPs. You will have to parse those coded alleles and combine with the reference allele contained in snp132 and the orthologous panTro2 allele (used to determine Ancestral allele) in order to get actual base values of Neandertal SNPs. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 10/23/2011 6:00 AM, Ravi Gupta wrote: > Dear HelpDesk, > > I was wondering whether UCSC provide a file using which I can obtain human > orthologus allele information from Neandertal, Chimp, Macaque, Orangutan, > Rhesus. > > Thanks. > --- > Regards > > Ravi Gupta, Ph.D. > Staff Scientist > Center for Systems& Computational Biology > Molecular and Cellular Oncogenesis Program > The Wistar Institute > 3601 Spruce Street > Philadelphia, PA 19104, USA > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
