Good Afternoon Starr: I'm curious what type of display you are expecting from your GTF file ? The UCSC browser can only display one name for an item. There isn't any data format that the browser can display that will contain the item name and the extra TCONS name that you mention. Is your GTF file tab-separated for the fields except for column 9 which separates its fields with blanks ?
--Hiram Starr Hazard wrote: > Folks, > > I have tried pasting several GTF files (my merged gtf from > cufflinks/cuffmerge) into the UCSC Genome browser. > > I can add some header lines to the GTF file, eg: > > browser position chr2:1-20000 > browser full 'Assembly' 'Ensembl Genes' 'RefSeq Genes' 'miRNA' > track name=Cufflinks description=merged.gtf > > then the regular gtf data. > Rat genome annotations seem to refer to chromosomes as "1" , "2" etc > not "chr1" ,"chr2" etc. > I fixed all the chromosome names to include the "chr" prefix with an > awk script. > > The header lines are accepted by the UCSC Genome browser but so far I > keep getting this error off the UCSC browser when the reader gets to > the first line of data > > *Error File 'chrxaa_test.txt' - Unrecognized format line 4 of custom > track: chr1 Cufflinks exon 12821949 12822044 . + . gene_id XLOC_000055; > transcript_id TCONS_00000116; exon_number 1; gene_name Txlnb; oId > ENSRNOT00000016553; nearest_ref ENSRNOT00000016553; class_code =; tss_id > TSS82; p_id P50; (note: chrom names are case sensitive) > > * > I want to use**the merged.gtf file since it contains the TCONS_### > and coordinates. > > I have tried adding header lines (browser and track lines), amending the > chromosome names, converting all spaces to tabs and just loading the > un-modified GTF from cuffmerge. All efforts result in the first line of > data confusing the UCSC browser. > > The GTF format is listed as one that UCSC Genome Browser can read and > use for a custom track but so far its not working for me. The first 8 > fields are standard but the 9th field have a variable format . > > I just spent about half an hour converting > (https://lists.soe.ucsc.edu/pipermail/genome/2011-April/025696.html) my > merged GTF to BigBed format to see if that worked but in the end I had > lost the TCONS labels which is what I want to try to display... > > Any suggestions? > > Starr _______________________________________________ Genome maillist - Genome@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
