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
