Thanks for the links. I updated to the latest version. What I noticed, though, is that some queries that map with the web interface don't map with the executable.
My parameters are : -q=dna -t=dna -minScore=54 -stepSize=5 -tileSize=10 -repMatch=2253 I was considering the sequence : >ASHG19A3A007737 TCTCGATGCGCCGTCGCCGGGTCAGCCGTTTCCTCTCCCTCGCCGGCCTCGGCGGAGATT it does not appear in my output PSL file. But if I paste it into the web interface I get : ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN --------------------------------------------------------------------------------------------------- browser details YourSeq 59 1 60 60 100.0% 17 + 46669702 46681323 11622 I am mapping against hg19 in both cases. $ blat blat - Standalone BLAT v. 34x12 fast sequence search command line tool What could be causing these to get dropped from the results ? ---- Original message ---- >Date: Fri, 27 Apr 2012 12:15:02 -0700 >From: Brooke Rhead <[email protected]> >Subject: Re: [Genome] blat minScore Unexpected Behaviour >To: [email protected] >Cc: [email protected] > >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 -------------------------------------- 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
