Hi, Tom! The native format for BLAT is psl. And BLAT chains together exons since it was designed for aligning mRNA to genomes.
However many of the alternate output types that BLAT provides will break the original chained psl alignment up so that it outputs a separate individual record for each exon. -Galt On Fri, Jul 27, 2012 at 9:51 PM, wangdp <[email protected]> wrote: > Dear Sir/Madam, > > > When I am using the local BLAT program to search the query against the > target sequence, I found very different results from the format blast9 and > psl. > > The blast9 results generate more than ten times hits than psl results. > > > Could you please help me about this? > > Thanks, > > With best, > > Tom > > 2012-07-28 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
