Hello Peng, This is the expected result. The browser uses a zero-based start position. Technically, this is a zero-based, half-open coordinate system. BLAT, when it produces output in a UCSC format such as PSL, the data will use the 0-based start.
http://genome.ucsc.edu/FAQ/FAQformat.html#format2 The web BLAT display shows the 1-based start is the output type is "link". If PSL is chosen instead, the format would be 0-based. Some details of this coordinate system are described here: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms 0-based, half-open = 0-25 = alignment length is 25 bases 1-based, closed = 1-25 = alignment length is 25 bases This can be a bit confusing at first. A good way to check which coordinate system is used to is compare the length of the alignment against the coordinates. When 0-based, it will appear at first glance as if the alignment coordinates produce a hit that is 1 base longer than the match length, unless the 0-based start is considered. Our apologies for any confusion this may have caused, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/19/10 4:09 PM, Peng Yu wrote: > BLAT gaggaaacgttcaccctgtctacta on ucsc website gives me. > > ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO > STRAND START END SPAN > --------------------------------------------------------------------------------------------------- > browser details YourSeq 25 1 25 25 100.0% 6 > + 87859757 87859781 25 > > > I run BLAT on command line. It gives me > > > 25 0 0 0 0 0 0 0 + > 486:557:1415670_at 25 0 25 chr6 149517037 > 87859756 87859781 1 25, 0, 87859756, > gaggaaacgttcaccctgtctacta, gaggaaacgttcaccctgtctacta, > > > The starts are off by 1. Could you please let me know why there is a > difference? Here is the version of my command line BLAT > > blat - Standalone BLAT v. 34 fast sequence search command line tool > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
