Arthur, Just in case I over explained that... the + strand coordinates are listed in the chain file as well. Just see the tStart and tEnd. And check here for more info:
http://genome.ucsc.edu/goldenPath/help/chain.html - Greg On 11/1/11 2:55 PM, Greg Roe wrote: > Hi Arthur, > > You are not seeing chain ID 439388 (listed at chr2:192280692-192283466) > in the browser at those coordinates because it is on the negative > strand. Note that in chain files (from: > http://genome.ucsc.edu/goldenPath/help/chain.html), " when the strand > value is "-", position coordinates are listed in terms of the > reverse-complemented sequence." > > To get the "browser coordinates" (+) from the file (where RC=reverse > compliment): > > StartRC = qSize - qEnd > EndRC = qSize - qStart > > So for the chain in question: > > chain 63452 chr2 242951149 + 50667683 50670457 chr2 242951149 - 192280692 > 192283466 439388 > > > You would find it here in the browser: > chr2:50,667,684-50,670,457 > > Please let us know if you have any additional questions: [email protected] > > - > Greg Roe > UCSC Genome Bioinformatics Group > > > > > > On 10/31/11 12:45 AM, arthur zhou wrote: >> dear Sir, >> I have a problem on the UCSC human genome data about self-chain. >> >> I download the data: hg18.hg18.net.gz, hg18.hg18.all.chain.gz, >> &chr#.hg18.hg18.net.axt.gz >> through http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsSelf/. >> >> Then I found a position: chr2:50667684-50670457 in the UCSC Genome >> Browser. Its self alignment is itself. >> >> Then when I check it in the data downloaded, in hg18.hg18.all.chain.gz I >> just found a position chr2:192280692-192283466, which it said they are a >> couple of self-chain. >> >> But i was surprised to find that I put the >> position chr2:192280692-192283466 into UCSC Genome Browser, there was no >> self-chain displayed. >> >> Did I download wrong data sets, or maybe there is a updated one needed? >> >> I appreciate your reply soon. >> >> your sincerely >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
