But I am not clear about the requisite parameters for running BLAT. Can we do the same exercise with BLAST also ?
The thing to note is that now both the longer reads (database) and the shorter reads (queries) belong to the same genotype (variety). The difference being that longer reads would be have lesser depth than the shorter ones. Isnt it? thanks On Tue, Sep 8, 2009 at 8:49 PM, Galt Barber <[email protected]>wrote: > > With 600,000 I think it will work. > We have used blat with 400,000 scaffolds before. > Speed might be slower than it is > with a typical chromosome-based assembly, > but I think it could still work for you. > Please let us know if you are successful. > > -Galt > > > > On Tue, 8 Sep 2009, Mera Vigyan wrote: > > 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
