Good Morning Matt: Are you perhaps observing the 'off-by-1' coordinate FAQ: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms
--Hiram Matthew Schu wrote: > Hello, > I created a local Blat server according to the instructions given in the FAQ > section of your site. When comparing the results of my query, which were > returned in psl format, to the results that the online Blat server would > return I noticed that the two returned different values for the qStart > positions, yet the qEnd positions were identical. The local server I set up > seems to give the position of the first base pair match of the query > sequence on the genome, however the online Blat server returns the position > of the base before the first match of the query sequence and the genome. > Can anyone tell me why there is a difference and why the online Blat server > returns the position of the base that is exactly one before the first > matching base? > > > Thank you, > > Matt Schu > Bioinformatics Grad. Student > Boston University _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
