Hello Chirag, Typically we must convert from GTF to another form to use it in the browser. Please see this previously answered mailing list question regarding conversion of GTF to BED:
https://lists.soe.ucsc.edu/pipermail/genome/2011-April/025696.html Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/28/11 4:55 AM, Chirag Nepal wrote: > Hi UCSC team, > > I was wondering what tool/package does UCSC use to convert the GTF > annotations to BED-12 file. > I would like to convert the GTF files (output from Cufflink) into bed file. > Could you suggest me which tools to use for the conversion purpose of GTF to > BED-12 file. > > Secondly, how are GTF files stored in the local UCSC browser. > I can see many loading script, such as hgLoadBed, hgLoadMAF and so on in > Jame;s Kent package, but did not find the loader script to load GTF files. > Could you please suggest me which script is used to load GTF files into the > local database. > > regards > Chirag > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
