On Tue, Sep 8, 2009 at 8:41 PM, Galt Barber <[email protected]>wrote:
> > How many long reads do you have? > > about 600,000 reads that is 300,000 paired reads Can we consider the set of these reads as a database ? The shorter reads are in very large number. thanks 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
