Hello Nirmala, The "bigDataUrl=..." type input only works with bigBed/bigWig files. You can read more about how to properly upload and format GTF custom tracks here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#GTF http://genome.ucsc.edu/goldenPath/help/customTrack.html#GFF And you can see examples that use the bigDataUrl syntax here: http://genome.ucsc.edu/goldenPath/help/bigWig.html http://genome.ucsc.edu/goldenPath/help/bigBed.html Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/2/11 10:16 AM, Akula, Nirmala (NIH/NIMH) [C] wrote: > Hi, > > I would like to upload rnaseq.combined.gtf file generated from cufflinks to > the browser. The file is on a ftp server. Here is the upload command I am > using: > > track name="chrY.gtf" description="chrY.gtf" > bigDataUrl=http://helixweb.nih.gov/ftp/pub/nimmi/4cases_5controls_individualLanes_pe_hg19_cuffcompare_withoutUcscGTF_chrYonly_forbrowser.combined.gtf > > The format of the GTF file is given below: > > -------------------------------------------------------------------------------------------------------------------------- > > track name="chrY.gtf" description="chrY.gtf" > chrY Cufflinks exon 2709637 2709668 . + . > gene_id "XLOC_127504"; transcript_id "TCONS_01000817"; exon_number "1"; oId > "CUFF.50723.1"; tss_id "TSS176374"; > chrY Cufflinks exon 2710206 2710283 . + . > gene_id "XLOC_127504"; transcript_id "TCONS_01000817"; exon_number "2"; oId > "CUFF.50723.1"; tss_id "TSS176374"; > chrY Cufflinks exon 2712118 2712298 . + . > gene_id "XLOC_127504"; transcript_id "TCONS_01000817"; exon_number "3"; oId > "CUFF.50723.1"; tss_id "TSS176374"; > > > --------------------------------------------------------------------------------------------------------------------------- > > The command does not generate any errors but the track is not visible. Do I > have to format the GTF file? > > Thank you very much. > > Regards, > Nirmala > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
