Hi Aaron, Would you please send a specific example: 1 the genome/version 2 that assembly's browser genomic coordinates you are comparing the refFlat data to 3 RefSeq sequence name/accession number 4 lines from refFlat file with the suspect alignment(s) 5 the exact location where you downloaded the refFlat and date of download
You can just send the data to me, not the entire list. We will investigate and provide help. Thank you, Jennifer Jackson UCSC Genome Bioinformatics Group Aaron Skewes wrote: > Hi, > > > > I am attempting to extract the nucleotide sequences for exons in several > genomes based on their locations listed in the refFlat.txt. In almost all > cases, the exonStarts-exonEnds do not correspond to the nucleotide position > relative to the refSeq for that particular organism and chromosome. For > example, mouse build37 has a 30Mbp gap at the start of all chromosomes, > except for Y. This gap is shown in the sequence with "N" but that is omitted > from the refFlat table. In other words, nucleotide position 30x10^6 + 1 = > position 0 in the refFlat. In chicken (and others), there are gaps > interspersed throughout many of the assembled chromosomes, shown with "N", > but refFlat locations are not offset by the gap lengths. > > > > Can somebody please suggest to me how I can extract genomic features based > on nucleotide position programmatically, if the refFlat positions do not > match the nucleotide positions and the offsets are unknown? > > > > Thank you, > > Aaron > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
