Hi, Fahim Here is the command we used to make our rat ooc.
blat rn5.2bit /dev/null /dev/null -tileSize=11 -makeOoc=rn5.11.ooc -repMatch=1100 Then, after that you would include this additional blat option: -ooc=rn5.11.ooc It's definitely worth a try. -Galt 11/30/2010 7:26 AM, Mohammad Fahim: > Hi > I am using standalone BLAT for querying est sequences againt human, > mouse and rat genome. > > I am using the following command: > > './blatDir/blat -noHead databaseFiles queryFile tmpPslFile' > > here the database and query files are in FASTA format. > > I blat for rat est squences (total est sequence for rat is around a > million) but it is taking time in days. I am intimidated by the toughts > when I will start doing it for human and mouse. > > Can I do something to tune the parameters so that it becomes even more > fast(I am becoming more greedy). > > In one of the archives it is recommended to use ooC file but since BLAT > internally create it, do I really need to do that? > > Thanks and regards > Fahim > Grad Student > University of Louisville > KY-USA > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
