---------- 已转发邮件 ---------- 发件人： arthur zhou <[email protected]> 日期： 2011年12月13日 下午7:44 主题： [Genome] a question for NNNNN-sequence 收件人： Greg Roe <[email protected]>
Dear Sir, when i browse the UCSC Genome Browser, I often found some regions that have no structure variation annotations (Segmental Duplication, self-chain, and so on). And its sequence is showed as NNNNNNNNNNN. A example is chr1: 167192 -217292 (HG18). So i really confused about why these sequence come, and can I get some file to know their locations？ Thank you so much. Hope you'll reply soon. Your sincerely Arthur 2011/11/15 arthur zhou <[email protected]> > Thank you so much for your reply. Its really a good help! > :) > > > 2011/11/15 Greg Roe <[email protected]> > >> Hi Arthur, >> >> Yes, they are both then in the same orientation = on the positive strand. >> >> The two assemblies in the chain track are referred to target and query. >> Target is the assembly you're on, and query the assembly you're finding a >> "match" on. Since this is the hg18 self-chain, both are hg18. The track >> description explains in more detail what is displayed in the self chain: >> >> "After filtering out the "trivial" alignments produced when identical >> locations of the genome map to one another (e.g. chr*N* mapping to chr*N*), >> the remaining alignments point out areas of duplication within the human >> [hg18] genome." >> >> I hope that helps. Please let us know if you have any additional >> questions: [email protected] >> >> >> - >> Greg Roe >> UCSC Genome Bioinformatics Group >> >> On 11/1/11 8:16 PM, arthur zhou wrote: >> >> Dear Sir, >> Thank you so much for your reply, which resolve my long-time problem. >> >> Now I have another question: >> >> When, the two strands are "+" and "+", does it mean they have the same >> orientation? >> Or I misunderstand the meaning of "reference"&"query". >> >> Thank you so much for your time and patience! >> >> Your sincerely >> >> Arthur >> >> 2011/11/2 Greg Roe <[email protected]> >> >>> 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 >>> >>> >>> >> >> >> -- >> Regards! >> >> Zhou Weichen >> >> MOE Key Laboratory of Contemporary Anthropology(Fudan University) >> >> School of Life-science at Fudan University >> >> 220# Handan Road, Shanghai(200433) >> >> P.R.China. >> >> > > > -- > Regards! > > Zhou Weichen > > MOE Key Laboratory of Contemporary Anthropology(Fudan University) > > School of Life-science at Fudan University > > 220# Handan Road, Shanghai(200433) > > P.R.China. > > -- Regards! Zhou Weichen MOE Key Laboratory of Contemporary Anthropology(Fudan University) School of Life-science at Fudan University 220# Handan Road, Shanghai(200433) P.R.China. -- Regards! Zhou Weichen MOE Key Laboratory of Contemporary Anthropology(Fudan University) School of Life-science at Fudan University 220# Handan Road, Shanghai(200433) P.R.China. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
