Hello Perdeep, Please see this FAQ for an answer to your second question: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1
Also, here is a description of PSL format: http://genome.ucsc.edu/FAQ/FAQformat#format2 Our mailing list software strips all attachments. If you would like to send your spreadsheet just to me (no need to cc the entire list) or just send a sample few lines that illustrates the confusing behavior, we can take a look and try to explain what is happening. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/05/08 12:40, Mehta, Perdeep wrote: > Hi, > > I have been testing standalone BLAT to search genomic locations for > 13 mouse sequences in a test set. In the output file in psl format I have two confusing things. First the target genomic start location for target does not always occur in column named "T start". Depending on the orientation of the target strand, + or - it corresponds to the start either in "T start" or "T end" column. This is fine I can deal with that, but for some reason one entry "t12" on row 16 (see attached spreadsheet) the target start and end are reversed that is no longer consistent with the rest of the entries. > > And why the target start is one base less compared to what I see on the ucsc browser for those sequences that have genes on + or sense strands? The target start of the standalone Blat does not match Blat results on ucsc browser. > > I will appreciate any help. > > thanks, > perdeep > > Perdeep K. Mehta, PhD > Research Informatics, Information Sciences Division > St. Jude Children's Research Hospital > 262 Danny Thomas Place > Memphis, TN 38105-2794 > Tel: 901-595 3774 > http://www.hatwellcenter.org/ > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
