Hi Julien, It seems your data is not in the correct format. The file you provided contains GTF lines (not GFF). The attribute list (9th column) must begin with two mandatory attributes: gene_id and transcript_id. The Genome Browser groups together GTF lines that have the same transcript_id value. Please see http://genome.ucsc.edu/goldenPath/help/customTrack.html#GTF for more information.
Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 9/27/2011 2:26 AM, Julien Lagarde wrote: > Hello UCSC, > > I'm having trouble displaying the following GFF custom track in the genome > browser (i tried both the official and the test browsers, hg19): > > chr1 cuff gene 121378993 121485462 . + > . gene_id "CUFF.10778"; nb_ov_gencgn: 0 > chr1 cuff gene 121484294 121485454 . - > . gene_id "CUFF.10779"; nb_ov_gencgn: 0 > chr1 cuff gene 148354447 148567575 . - > . gene_id "CUFF.11922"; nb_ov_gencgn: 0 > chr10 cuff gene 135502725 135524774 . - > . gene_id "CUFF.31198"; nb_ov_gencgn: 0 > chr13 cuff gene 114628641 114639949 . - > . gene_id "CUFF.62107"; nb_ov_gencgn: 0 > chr15 cuff gene 20844694 20961295 . - > . gene_id "CUFF.71392"; nb_ov_gencgn: 0 > chr15 cuff gene 84978946 85046757 . + > . gene_id "CUFF.77791"; nb_ov_gencgn: 0 > chr15 cuff gene 84979769 85047296 . + > . gene_id "CUFF.77793"; nb_ov_gencgn: 0 > chr15 cuff gene 102521102 102521395 . - > . gene_id "CUFF.79297"; nb_ov_gencgn: 0 > chr2 cuff gene 87666667 87761847 . - > . gene_id "CUFF.115945"; nb_ov_gencgn: 0 > chr21 cuff gene 9534417 9838921 . - . gene_id > "CUFF.136016"; nb_ov_gencgn: 0 > chr21 cuff gene 9689384 9934002 . + . gene_id > "CUFF.136053"; nb_ov_gencgn: 0 > chr21 cuff gene 9700746 9880280 . - . gene_id > "CUFF.136024"; nb_ov_gencgn: 0 > chr21 cuff gene 9702704 9902649 . + . gene_id > "CUFF.136054"; nb_ov_gencgn: 0 > chr21 cuff gene 9740900 9891176 . + . gene_id > "CUFF.136095"; nb_ov_gencgn: 0 > chr21 cuff gene 11162794 11188149 . + > . gene_id "CUFF.134755"; nb_ov_gencgn: 0 > chr4 cuff gene 40296208 40297816 . + > . gene_id "CUFF.162499"; nb_ov_gencgn: 0 > chr4 cuff gene 191043606 191044278 . - > . gene_id "CUFF.175666"; nb_ov_gencgn: 0 > chr7 cuff gene 61266265 61586663 . + > . gene_id "CUFF.211570"; nb_ov_gencgn: 0 > chrX cuff gene 2066385 2068239 . - . gene_id > "CUFF.244905"; nb_ov_gencgn: 0 > chrX cuff gene 7511069 7806153 . + . gene_id > "CUFF.245203"; nb_ov_gencgn: 0 > > (i've also attached the original GFF file) > > upon uploading it, there is no error message, however the custom track does > not show up in the browser. > > thanks > j > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
