Hi Arthur, The NNNNs that you are seeing are from gaps. You can see this by displaying the gap track in the browser.
To download all of the positions in the gap track, you can use our table browser tool. To get to the table browser click the "Tables" link from the blue navigation bar. If you are unfamiliar with the table browser, please refer to the user's guide: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html and the following tutorial: http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml If you have further questions, please email the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: arthur zhou <[email protected]> Date: 2011/12/13 Subject: [Genome] Fwd: a question for NNNNN-sequence To: [email protected] ---------- 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
