Hello Preeti, Please see this online help doc for an explanation of how to use PSL files as Custom Tracks: http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL
I hope this information is helpful to you. Please don't hesitate to contact the mail list again if you require further assistance. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu Sankaranarayanan Preethi wrote: > > Hi Hiram, > > Thank you for responding. But when I tried to run it > through the table browzer, i get the following error. > > Error File 'ref1.psl.txt' - Error line 6 of custom track: 1 > not a recognized sequence (note: sequence names are case > sensitive) > > I have also attached the file with just one line on it. > Could you please help? > > Thanks, > Preeti > >> --- On Sat, 14/11/09, Hiram Clawson <[email protected]> >> wrote: >> >>> From: Hiram Clawson <[email protected]> >>> Subject: Re: [Genome] psltobed.c >>> To: "Sankaranarayanan Preethi" <[email protected]> >>> Cc: [email protected] >>> Date: Saturday, 14 November, 2009, 12:04 PM >>> Good Evening Preethi: >>> >>> This is a program in the kent source tree. >>> http://genome.ucsc.edu/admin/cvs.html >>> http://genome.ucsc.edu/admin/jk-install.html >>> >>> It would be easier to enter your psl file as a custom >>> track into the genome browser, then use the table >>> browser to dump it back to you as a bed file. >>> http://genome.ucsc.edu/goldenPath/help/customTrack.html >>> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html >>> >>> --Hiram >>> >>> >>> Sankaranarayanan Preethi wrote: >>>> Hi, >>>> >>>> I have no idea where should I download this file >> and >>> run. My problem is I have a .psl file. I need to >> convert it >>> to a .bed file. that is all. Could you please help me >> how to >>> do this? I tried checking on the genome browser >> webpage. >>> there is no download... I am confused. please help! >>>> Thanks, >>>> Preeti >>>> >>>> >>>> Add whatever you love >>> to the Yahoo! India homepage. Try now! http://in.yahoo.com/trynew >>>> _______________________________________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>> >> >> Yahoo! India has a new look. Take a >> sneak peek http://in.yahoo.com/trynew > > > Try the new Yahoo! India Homepage. Click here. > http://in.yahoo.com/trynew > > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
