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 - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
