Hi Daisuke, These files are now available: /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/vsSelf/axtNet/*
Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Vanessa Kirkup Swing" <[email protected]> To: "Daisuke Komura" <[email protected]> Cc: [email protected] Sent: Friday, April 15, 2011 3:05:37 PM Subject: Re: [Genome] self-chain for hg19 Hi Daisuke, We have many utilities available for public use (http://genomewiki.ucsc.edu/index.php/Kent_source_utilities). There is a utility available called netToAxt that converts net files to axt files. This utility can be obtained by downloading our source code (http://genome.ucsc.edu/FAQ/FAQlicense#license3). We have the file you are interested in converting on our list of things to do. We will get back to you when it is available. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Daisuke Komura" <[email protected]> To: "Mary Goldman" <[email protected]> Cc: [email protected] Sent: Thursday, April 14, 2011 3:11:51 AM Subject: Re: [Genome] self-chain for hg19 Hi Mary, Thank you, but what I really want is axt files. Could you also upload them or tell me how to convert the net file to axt files? Best, Daisuke Komura ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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] ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2011/4/14 Mary Goldman <[email protected]>: > Hi Daisuke, > > Thank you for your patience. We have now uploaded the net file to here: > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsSelf/hg19.hg19.net.gz. > > If you have any other comments or questions, please feel free to contact the > mailing list again ([email protected]). > > Best, > Mary > --------------------- > Mary Goldman > UCSC Bioinformatics Group > > On 4/5/11 2:33 PM, Daisuke Komura wrote: >> >> Dear Luvina, >> >> Could you please also upload best-chain alignments in axt format for >> hg19 like hg18? >> Those for hg18 is found in the following URL. >> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsSelf/axtNet/ >> >> Thank you in advance, >> Daisuke >> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ >> 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] >> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ >> >>> 2011/3/2 Luvina Guruvadoo<[email protected]>: >>>> >>>> Hi Daisuke, >>>> >>>> Our apologies, Human self alignments for hg19 was missing from the >>>> downloads >>>> page. The download file has been added and can be found here: >>>> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsSelf/. >>>> >>>> Regards, >>>> Luvina >>>> >>>> --- >>>> Luvina Guruvadoo >>>> UCSC Genome Bioinformatics Group >>>> >>>> >>>> Daisuke Komura wrote: >>>>> >>>>> Hello, >>>>> >>>>> Can anyone tell me if it is possible to download Human self alignments >>>>> for hg19? >>>>> I found that for hg18 in >>>>> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsSelf/ but can't find >>>>> that for hg19. >>>>> Thank you. >>>>> >>>>> Daisuke Komura >>>>> 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
