Hi Monitha, The following page on our Wiki should provide some clarification: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms
This page may also be useful for you: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 Feel free to contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 7/26/2012 6:51 AM, monithamohan harilkumar wrote: > Hello, > > My earlier mails egarding lift over were cleared well. Now i have a doubt > regarding SNP table from UCSC > > My data,its a methylation data and i need to check if the methylation is > just an SNP or not , is positioned in this way- For e.g. > hg18mapinfo strand > 100532397 top > 149364056 bot > 23982732 bot > 53478180 bot > > > > > the snp data which i retrieved as you knwo will have following col > hg18start(chrom start) hg18end(chrom end) (and a few other col > ...which is not relevant right now) > > 100532397 100532398 > 1493640565 149364056 > 23982731 23982732 > 53478180 53478180 > > > whien i map between these two tables..as I told you i need to check for > SNPs in my methylation data, I get is > > hg18start(chrom start) hg18end(chrom end) hg18mapinfo > strand > 100532397 100532398 > 100532397 top > 1493640565 149364056 > 149364056 bot > 23982731 23982732 > 23982732 > bot > 53478180 53478181 > 53478180 > bot > > As you can see mapping is done in between start and end posiitons this is > causing me confusion , what should i understand from this, I need all the > positions that has C , but when it maps like this with start or end, I dont > understand.and i dont know how to assign the remaining coloumns. > The basic doubt is , isnt there an SNP table with just one location for one > base pair, because these two start and end correspond to two different base > pairs in actual gene. > > Thanks, > Monitha > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
