Hi Adrian, You can get some of this information from the cosmicRaw table in the Table Browser... hg19 group: Phenotype and Disease Associations track: cosmic table: cosmicRaw
Click on the "describe table schema" button to see what data is there and how it's displayed. (Exon number and strand info is not there. I don't believe COSMIC keeps strand info and we do not have exon numbers available in the format you're looking for. Galaxy may have a tool that provides this info: https://main.g2.bx.psu.edu/) To enter your list, click the filter button. You can list the cDNA ids (e.g. c.1879G>A) in a space separated list in the text field to the right of " mut_syntax_cds". Protein ids go next to " mut_syntax_aa ". However, you will have to do the cDNA and protein queries separately (one at a time), as if you do them both at once, it will only return rows that match both lists, and I doubt that's what you want. You also might want to try contacting COSMIC directly (http://www.sanger.ac.uk/genetics/CGP/cosmic/) to see if they have the raw data which might include strand and exon numbers. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 5/19/12 10:52 AM, Adrian Johnson wrote: > Hi: > > I have list of cosmic mutations in cDNA and protein format. > > Such as : > > c.1879G>A and p.A627T for gene SMO and NM_005631. > > I want to get the following information using table browser. > > 1. Exon # > 2. a dbSNP ID rs****** IF present > 3. codon information GCT> ACT (here G> A substitution happened) > 4. strand information > 5.and position chr7:128851554 > > > You help will be very useful to me. > > Thanks and I appreciate your help. > > -Adrian > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
