Hello Gang, We are unable to reproduce the error you are seeing and we also recently experienced temporary issues with our site. Please let us know if you are still having this problem.
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 05/31/11 17:02, Gang Wei wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
