Dear manager of UCSC Genome Browser, Glad to write to you. I'm now using UCSC genome browser to check the assembled transcripts derived from RNA-seq data. UCSC genome browser usually works quite well for my purpose, but since last Friday, the gtf file can NOT be upload onto UCSC genome browser, but other files can.
the GTF file format(which also shows as follows) I used is just as those I used before, but it is very weird that now causing errors like: Error 500: Internal Server Error The page you requested resulted in a server problem on our systems. We hate this type of error immensely and we're sure that you do as well. While we have logged it and rapidly pursue any problems on our systems, sometimes extra information from the user can pinpoint the cause of the problem for us and help us prevent it in the future. If you have information that you would like to provide about what led to the error, please email us at [email protected]. If you are unable to access commonly-used features on our website, it is possible that you may need to reset your Genome Browser with the following URL: http://genome.ucsc.edu/cgi-bin/cartReset. This will replace your stored settings with the default configuration and will return your Browser to the state it was in when you first accessed it. We apologize for the inconvenience. The GTF file format I used is as follows track name="my.combined.gtf" description="my.combined.gtf" chr1 hg19_knownGene exon 322037 322228 . + . gene_id "XLOC_000001"; transcript_id "5_00000001"; exon_number "1"; gene_name "uc009vjk.2"; oId "uc009vjk.2"; nearest_ref "uc009vjk.2"; class_code "="; tss_id "TSS1"; p_id "P1"; chr1 hg19_knownGene exon 324288 324345 . + . gene_id "XLOC_000001"; transcript_id "5_00000001"; exon_number "2"; gene_name "uc009vjk.2"; oId "uc009vjk.2"; nearest_ref "uc009vjk.2"; class_code "="; tss_id "TSS1"; p_id "P1"; chr1 hg19_knownGene exon 324439 326938 . + . gene_id "XLOC_000001"; transcript_id "5_00000001"; exon_number "3"; gene_name "uc009vjk.2"; oId "uc009vjk.2"; nearest_ref "uc009vjk.2"; class_code "="; tss_id "TSS1"; p_id "P1"; chr1 hg19_knownGene exon 323892 324060 . + . gene_id "XLOC_000001"; transcript_id "5_00000003"; exon_number "1"; gene_name "uc001aav.3"; oId "uc001aav.3"; nearest_ref "uc001aav.3"; class_code "="; tss_id "TSS2"; chr1 hg19_knownGene exon 324288 324345 . + . gene_id "XLOC_000001"; transcript_id "5_00000003"; exon_number "2"; gene_name "uc001aav.3"; oId "uc001aav.3"; nearest_ref "uc001aav.3"; class_code "="; tss_id "TSS2"; chr1 hg19_knownGene exon 324439 326938 . + . gene_id "XLOC_000001"; transcript_id "5_00000003"; exon_number "3"; gene_name "uc001aav.3"; oId "uc001aav.3"; nearest_ref "uc001aav.3"; class_code "="; tss_id "TSS2"; chr1 hg19_knownGene exon 327036 328580 . + . gene_id "XLOC_000001"; transcript_id "5_00000003"; exon_number "4"; gene_name "uc001aav.3"; oId "uc001aav.3"; nearest_ref "uc001aav.3"; class_code "="; tss_id "TSS2"; chr1 hg19_knownGene exon 323892 324060 . + . gene_id "XLOC_000001"; transcript_id "5_00000002"; exon_number "1"; gene_name "uc001aau.2"; oId "uc001aau.2"; nearest_ref "uc001aau.2"; class_code "="; tss_id "TSS2"; p_id "P1"; chr1 hg19_knownGene exon 324288 324345 . + . gene_id "XLOC_000001"; transcript_id "5_00000002"; exon_number "2"; gene_name "uc001aau.2"; oId "uc001aau.2"; nearest_ref "uc001aau.2"; class_code "="; tss_id "TSS2"; p_id "P1"; Could you help find anything wrong with my file or any bugs happened to UCSC genome browser. Thanks, Gang Wei, Ph.D The State Key Laboratory of Genetic Engineering, Institute of Life Sciences, Fudan University, Shanghai, 200433, China Email: [email protected] Computational Genomics Research Group Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA Email: [email protected]; [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
