How many long reads do you have? BLAT has been used on genomes with a few hundred thousand scaffolds.
But if you have millions or billions of long reads, I don't think BLAT would be the right tool. You might be able to lump the reads together into artificial chromosomes (possibly with gaps) thus reducing the number of elements in your database target to a manageable number. But this would require you to set up your own pre and post processing steps. Have you looked at maq, bowtie and other short-read aligners yet? Perhaps they would be helpful. -Galt On Mon, 7 Sep 2009, Mera Vigyan wrote: > greetings, > > Can we use the set of long reads as a reference database and > the set of short reads as queries and run BLAT in this fashion ? > > thanks > Mera > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
