Hi Dario, Increasing the -minScore to a number that is over half the query size has no further effect (at least in slightly older versions of blat). See the end of this FAQ:
http://genome.ucsc.edu/FAQ/FAQblat.html#blat8 There is some more background discussion in our mailing list archives, here: https://lists.soe.ucsc.edu/pipermail/genome/2010-April/022062.html We recommend using the pslReps or pslCdnaFilter programs on your blat results rather than setting the -minScore option. If you don't already have those programs, there are executables here: http://hgdownload.cse.ucsc.edu/admin/exe/ or you can get the source http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 4/26/12 9:00 PM, Dario Strbenac wrote: > I'm using the command blat with > > -minScore=60 > > and my file has all 60 base DNA sequences. They are actually microarray > probes. > > My version is > > $ blat > blat - Standalone BLAT v. 34 fast sequence search command line tool > > The documentation further down the screen says > > -minScore=N sets minimum score. This is the matches minus the mismatches > minus some sort of gap penalty. Default is 30 > > How can I possibly be getting any matches less than 60 bases then ? > > $ head -n 15 result.psl | cut -f 1,2 - > > match mis- > match > --------------- > 60 0 > 60 0 > 58 1 > 51 0 > 59 0 > 58 1 > 58 1 > 56 3 > 55 3 > 58 1 > > -------------------------------------- > Dario Strbenac > Research Assistant > Cancer Epigenetics > Garvan Institute of Medical Research > Darlinghurst NSW 2010 > Australia > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
