Good morning Gundala,
One easy way to get this data into BED format is to use the Table Browser, select the mm9 version of the table, and set the output format to "BED". I hope that helps! Please do contact us again if you run into any further problems. Kayla Smith UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Gundala Viswanath" <[email protected]> To: "Jennifer Jackson" <[email protected]> Cc: [email protected] Sent: Wednesday, March 11, 2009 7:49:13 AM GMT -08:00 US/Canada Pacific Subject: [Genome] Howto convert Acembly format to LiftOver Acceptable Format - was: Acembly File for MM8 Hi Jeniffer and all, Following your advice I intend to convert this acembly.txt from MM9: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/acembly.txt.gz into MM8, by uploading it to this website you suggested: http://genome.ucsc.edu/cgi-bin/hgLiftOver but somehow it fails to execute. Is there a way/tool where I can convert the acembly format into BED/Position format acceptable for the website? Yours, Gundala Viswanath On Wed, Mar 11, 2009 at 3:13 AM, Jennifer Jackson <[email protected]> wrote: > Hello, > > The "AceView Genes" track was included in the mm9 annotation set, but not in > mm8 (or mm7). > > To map individual genomic locations between assemblies, use the "Convert" > tool (top blue navigation bar) from within the starting assembly's browser > (in your case, mm9). > > To map larger data sets or entire tracks, the liftOver tool can be used. > There is a browser based version and a unix version. > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert > > Thank you, > Jennifer Jackson > UCSC Genome Bioinformatics Group > > Gundala Viswanath wrote: >> >> Dear all, >> >> I have no problem finding acembly.txt for MM9, >> but not for MM8. >> >> Is there a way I can download if? >> I can't find one in this url: >> >> http://hgdownload.cse.ucsc.edu/goldenPath/mm8/database/ >> >> - Gundala Viswanath >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
