Hi Paul, Here a link detailing the coordinate conventions: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms
Basically, for + strand alignments, add 1 to the start (smallest coordinate number) for the actual base position of the start of the alignment. For - strand alignments, the "start" is really the end, so add 1 to the smallest coordinate number for the actual base position of the end of the alignment. This can be confusing at first, but these are the main points: 1) genomic coordinates are stored smallest -> largest. If the strand is -, then the columns labels start/end should be actually interpreted as end/start. 2) for the smallest coordinate number, add one to have the actual physical position of the feature (could be the start or end of the feature, depending on strand). Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Paul Evans wrote: > Hi, > > I wanted to list all the exon start and end positions in the genome. I used > the 'Table Browser' (May 2004 assembly) to get to the details. A couple of > the rows are: > ---------------------------------------------------------------------------------------------- > #name chrom strand txStart txEnd cdsStart cdsEnd exonCount > exonStarts exonEnds > > > NR_026820 chr1 - 24474 25944 25944 25944 3 > 24474,25139,25583, 25037,25344,25944, > NM_001005484 chr1 + 58953 59871 58953 59871 1 > 58953, 59871, > ---------------------------------------------------------------------------------------------- > In both the '-' & '+' strands the exonStart postion to exonEnd position goes > from smaller -> higher number. So, for the 2 rows cited above, I can say: > Exon Start Exon End > ------------ ----------- > 24474 25037 > 25139 25344 > 25583 25944 > 58953 59871 > Would this be correct? > thanks! > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
