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/
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