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
