Hello Henrik, You have found what we believe to be a bug in the table browser. We are currently looking into it and will get back to you when we have tracked down a fix.
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 04/06/11 08:51, Henrik Stranneheim wrote: > Hi, > > I downloaded a GTF of refSeq Genes using the table browser. > > > It seems like some entries have start positions that are larger than > the stop positions, which I thought was not ment to be according to > the definition of the GTF. Is this a bug or can you give me an > explanation of why these features are listed this way? > > > perl -n -a -e'if (@F[3] > @F[4]) { print $_;}' RefSeq_hg19 > chr1 hg19_refGene CDS 92852568 92846428 0.000000 > + 1 gene_id > "NM_024813"; transcript_id "NM_024813"; > chr1 hg19_refGene CDS 151220339 151220338 0.000000 > + 0 gene_id > "NM_001135636"; transcript_id "NM_001135636"; > chr1 hg19_refGene CDS 151220339 151220338 0.000000 > + 0 gene_id > "NM_003557"; transcript_id "NM_003557"; > chr1 hg19_refGene CDS 151220339 151220338 0.000000 > + 0 gene_id > "NM_001135637"; transcript_id "NM_001135637"; > chr1 hg19_refGene CDS 151220339 151220338 0.000000 > + 0 gene_id > "NM_001135638"; transcript_id "NM_001135638"; > chr1 hg19_refGene CDS 228681584 228681583 0.000000 > + 0 gene_id > "NM_001010858"; transcript_id "NM_001010858"; > chr2 hg19_refGene CDS 234115352 234115351 0.000000 > + 1 gene_id > "NM_001017915"; transcript_id "NM_001017915"; > chr2 hg19_refGene CDS 234115352 234115351 0.000000 > + 1 gene_id > "NM_005541"; transcript_id "NM_005541"; > chr2 hg19_refGene CDS 71211741 71211378 0.000000 > + 2 gene_id > "NM_024933"; transcript_id "NM_024933"; > chr2 hg19_refGene CDS 86439549 86437734 0.000000 > + 1 gene_id > "NM_145644"; transcript_id "NM_145644"; > chr2 hg19_refGene CDS 96907615 96906424 0.000000 > + 1 gene_id > "NM_001037228"; transcript_id "NM_001037228"; > chr3 hg19_refGene CDS 77695205 77694054 0.000000 > + 2 gene_id > "NM_002942"; transcript_id "NM_002942"; > chr3 hg19_refGene CDS 77695205 77694054 0.000000 > + 1 gene_id > "NM_001128929"; transcript_id "NM_001128929"; > chr3 hg19_refGene CDS 109212986 109195607 0.000000 > + 1 gene_id > "NM_001145553"; transcript_id "NM_001145553"; > chr4 hg19_refGene CDS 2929898 2928400 0.000000 + 1 > gene_id > "NM_176801"; transcript_id "NM_176801"; > chr4 hg19_refGene CDS 2929898 2928400 0.000000 + 1 > gene_id > "NM_014190"; transcript_id "NM_014190"; > chr4 hg19_refGene CDS 70811914 70810720 0.000000 > + 1 gene_id > "NM_001890"; transcript_id "NM_001890"; > chr4 hg19_refGene CDS 70811914 70810720 0.000000 > + 1 gene_id > "NM_001025104"; transcript_id "NM_001025104"; > chr4 hg19_refGene CDS 186321171 186320925 0.000000 > + 1 gene_id > "NM_181726"; transcript_id "NM_181726"; > chr5 hg19_refGene CDS 52781517 52781056 0.000000 > + 2 gene_id > "NM_006350"; transcript_id "NM_006350"; > chr5 hg19_refGene CDS 53839009 53815555 0.000000 > + 2 gene_id > "NM_001145427"; transcript_id "NM_001145427"; > chr6 hg19_refGene CDS 46644384 46644383 0.000000 > + 0 gene_id > "NM_001204051"; transcript_id "NM_001204051"; > chr7 hg19_refGene CDS 66105381 66104213 0.000000 > + 1 gene_id > "NM_001167961"; transcript_id "NM_001167961"; > chr8 hg19_refGene CDS 30416404 30407100 0.000000 > + 1 gene_id > "NM_001008711"; transcript_id "NM_001008711"; > chr8 hg19_refGene CDS 19822821 19819728 0.000000 > + 1 gene_id > "NM_000237"; transcript_id "NM_000237"; > chr8 hg19_refGene CDS 24366059 24365046 0.000000 > + 1 gene_id > "NM_003817"; transcript_id "NM_003817"; > chr8 hg19_refGene CDS 80577050 80575895 0.000000 > + 2 gene_id > "NM_001199214"; transcript_id "NM_001199214"; > chr9 hg19_refGene CDS 71623363 71623362 0.000000 > + 0 gene_id > "NM_003558"; transcript_id "NM_003558"; > chrX hg19_refGene CDS 51079091 51076309 0.000000 > + 1 gene_id > "NM_153183"; transcript_id "NM_153183"; > chr10 hg19_refGene CDS 71718455 71718454 0.000000 > + 0 gene_id > "NM_080802"; transcript_id "NM_080802"; > chr10 hg19_refGene CDS 71718455 71718454 0.000000 > + 0 gene_id > "NM_080798"; transcript_id "NM_080798"; > chr10 hg19_refGene CDS 71718455 71718454 0.000000 > + 0 gene_id > "NM_080800"; transcript_id "NM_080800"; > chr10 hg19_refGene CDS 71718455 71718454 0.000000 > + 0 gene_id > "NM_080805"; transcript_id "NM_080805"; > chr10 hg19_refGene CDS 71718455 71718454 0.000000 > + 0 gene_id > "NM_001130103"; transcript_id "NM_001130103"; > chr10 hg19_refGene CDS 71718455 71718454 0.000000 > + 0 gene_id > "NM_080801"; transcript_id "NM_080801"; > chr10 hg19_refGene CDS 79799962 79799961 0.000000 > + 0 gene_id > "NM_033022"; transcript_id "NM_033022"; > chr10 hg19_refGene CDS 115540361 115535623 0.000000 > + 1 gene_id > "NM_024889"; transcript_id "NM_024889"; > chr14 hg19_refGene CDS 104167538 104167537 0.000000 > + 0 gene_id > "NM_001130107"; transcript_id "NM_001130107"; > chr15 hg19_refGene CDS 67599164 67599163 0.000000 > + 0 gene_id > "NM_022784"; transcript_id "NM_022784"; > chr15 hg19_refGene CDS 78829642 78819904 0.000000 > + 2 gene_id > "NM_001083612"; transcript_id "NM_001083612"; > chr16 hg19_refGene CDS 68260253 68260252 0.000000 > + 0 gene_id > "NM_173163"; transcript_id "NM_173163"; > chr16 hg19_refGene CDS 7760625 7759131 0.000000 + 1 > gene_id > "NM_145893"; transcript_id "NM_145893"; > chr16 hg19_refGene CDS 28884768 28884589 0.000000 > + 2 gene_id > "NM_001145797"; transcript_id "NM_001145797"; > chr17 hg19_refGene CDS 45759770 45758033 0.000000 > + 1 gene_id > "NM_002265"; transcript_id "NM_002265"; > chr17 hg19_refGene CDS 40948704 40948703 0.000000 > + 0 gene_id > "NM_032387"; transcript_id "NM_032387"; > chr18 hg19_refGene CDS 77287528 77287527 0.000000 > + 0 gene_id > "NM_172389"; transcript_id "NM_172389"; > chr18 hg19_refGene CDS 77287528 77287527 0.000000 > + 0 gene_id > "NM_006162"; transcript_id "NM_006162"; > chr18 hg19_refGene CDS 77287528 77287527 0.000000 > + 0 gene_id > "NM_172388"; transcript_id "NM_172388"; > chr18 hg19_refGene CDS 21741480 21740031 0.000000 > + 1 gene_id > "NM_153770"; transcript_id "NM_153770"; > chr18 hg19_refGene CDS 21741480 21740031 0.000000 > + 1 gene_id > "NM_138644"; transcript_id "NM_138644"; > chr18 hg19_refGene CDS 21741480 21740031 0.000000 > + 1 gene_id > "NM_138643"; transcript_id "NM_138643"; > chr18 hg19_refGene CDS 21741480 21740031 0.000000 > + 1 gene_id > "NM_153769"; transcript_id "NM_153769"; > chr19 hg19_refGene CDS 1278776 1277296 0.000000 + 1 > gene_id > "NM_017914"; transcript_id "NM_017914"; > chr19 hg19_refGene CDS 12024224 12015701 0.000000 > + 2 gene_id > "NM_021915"; transcript_id "NM_021915"; > chr20 hg19_refGene CDS 44002934 43994324 0.000000 > + 1 gene_id > "NM_001099791"; transcript_id "NM_001099791"; > chr21 hg19_refGene CDS 35209291 35208935 0.000000 > + 2 gene_id > "NM_001001132"; transcript_id "NM_001001132"; > chr22 hg19_refGene CDS 46239549 46239548 0.000000 > + 0 gene_id > "NM_013236"; transcript_id "NM_013236"; > chr22 hg19_refGene CDS 46239549 46239548 0.000000 > + 0 gene_id > "NM_001167621"; transcript_id "NM_001167621"; > > Cheers, > > Henrik Stranneheim > Ph.D. Student > Division of Gene Technology > Science for Life Laboratory, KISP > Royal Institute of Technology, KTH > SE-171 65 Solna, Sweden > > E-mail: [email protected] > Phone: +46 (0)8 524 81487 (Office) > Phone: +46 (0)736251487 (Mobile) > Visiting address: Tometebodavägen 23A > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
