Hello Bingbing, Thank you for reporting this error. It has been submitted as a correction to the development team. For now, just remove or ignore the "_dup1" portion of the sequence names.
If you do not see a resolution by mid-summer, please feel free to contact us for an update. I hope this information is helpful. And we very much apologize for the inconvenience this error has caused you. Best regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] On 6/11/10 9:31 AM, Bingbing Yuan wrote: > Hi, > I downloaded the hg18 refGene gff from UCSC table, and noticed that if a > refGene transcript was mapped to more than one locations, '_dup' was added to > the refGene ID. For example: NM_001005277_dup1. In the case of NM_001005277, > it mapped to 3 locations in genome, two of them mapped to chr1 and one mapped > to chr5. I thought it would be NM_001005277, NM_001005277_dup1, > NM_001005277_dup2. But actually, the gff file had NM_001005277, > NM_001005277_dup1, NM_001005277. Both chr1 and chr5 has the same > NM_001005277. Is this an error? If not, could you explain the rational > behind this? > > chr1 hg18_refGene start_codon 357522 357524 0.000000 + > . gene_id "NM_001005277"; transcript_id "NM_001005277"; > chr1 hg18_refGene CDS 357522 358457 0.000000 + 0 > gene_id "NM_001005277"; transcript_id "NM_001005277"; > chr1 hg18_refGene stop_codon 358458 358460 0.000000 + > . gene_id "NM_001005277"; transcript_id "NM_001005277"; > chr1 hg18_refGene exon 357522 358460 0.000000 + . > gene_id "NM_001005277"; transcript_id "NM_001005277"; > chr1 hg18_refGene stop_codon 610959 610961 0.000000 - > . gene_id "NM_001005277"; transcript_id "NM_001005277_dup1"; > chr1 hg18_refGene CDS 610962 611897 0.000000 - 0 > gene_id "NM_001005277"; transcript_id "NM_001005277_dup1"; > chr1 hg18_refGene start_codon 611895 611897 0.000000 - > . gene_id "NM_001005277"; transcript_id "NM_001005277_dup1"; > chr1 hg18_refGene exon 610959 611897 0.000000 - . > gene_id "NM_001005277"; transcript_id "NM_001005277_dup1"; > chr5 hg18_refGene start_codon 180726894 180726896 > 0.000000 + . gene_id "NM_001005277"; transcript_id > "NM_001005277"; > chr5 hg18_refGene CDS 180726894 180727829 0.000000 > + 0 gene_id "NM_001005277"; transcript_id "NM_001005277"; > chr5 hg18_refGene stop_codon 180727830 180727832 > 0.000000 + . gene_id "NM_001005277"; transcript_id > "NM_001005277"; > chr5 hg18_refGene exon 180726894 180727832 0.000000 > + . gene_id "NM_001005277"; transcript_id "NM_001005277"; > > Thanks, > Bingbing > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
