Hi Daisuke, I apologize for the delayed reply. I took a look at the two coordinates you listed below in the browser. The first position you give has several chains showing in the browser and I spot checked a couple and they were there in the file. The second position doesn't have any.
Can you give us the specific IDs of some chains that you cannot find in the file? Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 5/9/11 6:20 AM, Daisuke Komura wrote: > Dear Colleagues, > > I have two questions about human chained self alignments (hg19). > > 1. Axt files and hg19.hg19.all.chain.gz, which can be download from > the following address, do not seem to include many of chained self > alignments shown in the genome brower. Please see > chr17:37990980-37992472 and chr8:83871562-83873067 - 108685 in axt > files for example. Why? > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsSelf/ > > 2. Where can I download all the self-chain alignment information > (positions and the aligned sequences) shown in the genome browser? > > Thank you > > ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ > Daisuke Komura > Department of Pathology, Graduate School of Medicine, The University of Tokyo. > 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan > mailto:[email protected] > ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ > > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
