Thanks Galt. What is the version of blat that is being used. The reason we are asking this question is that Ismael found some inconsistencies between the web output and the stand-alone output. Thanks, Jack
On Mon, May 11, 2009 at 7:30 PM, Galt Barber <[email protected]>wrote: > > Actually this is how our gfServers are configured. > hgBlat cgi calls these. > > gfServer (this is how the UCSC web-based blat servers are configured): > > * blat server (capable of PCR): > gfServer start blatMachine portX -stepSize=5 -log=untrans.log > database.2bit > > * translated blat server: > gfServer start blatMachine portY -trans -mask -log=trans.log > database.2bit > > > The line you quoted is about how one run standalone > command-line blat to approximate the behavior of hgBlat/gfServer. > > -Galt > > > > On Mon, 11 May 2009, Ismael Vergara wrote: > > Hi, >> >> I would like to know which blatSuite release number is the one running >> behind >> >> http://genome.ucsc.edu/cgi-bin/hgBlat?command=start >> >> Also, I would like to confirm with you if the parameters used in the BLAT >> web server (according to the FAQ) are: >> >> blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 database.2bit >> query.fa output.psl >> >> Does this still applies as it is stated here? >> >> Thanks in advance, >> Ismael >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> -- Jack Chen, Ph.D., Associate Professor, MSFHR Scholar Molecular Biology and Biochemistry, Simon Fraser University SSB8111, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6 TEL: 778-782-4823; FAX: 778-782-558 http://www.sfu.ca/mbb/People/Chen/ http://genome.sfu.ca/orthoclusterdb/ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
