Hi Mera, As for query and target datasets, using the UCSC web blat, only genomic loaded as a target. On your own server, any dataset can be the target (reference database).
You might find it useful to tune parameters for this type of case (query = short reads, target = transcripts and/or expected genomic location) to get the best (most complete) alignment. See the BLAT documentation for options. Testing these out using your own test cases would be the best way to identify which parameters provide the most useful alignments. http://genome.ucsc.edu/FAQ/FAQblat.html Thanks, jen ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Mera Vigyan" <[email protected]> wrote: > From: "Mera Vigyan" <[email protected]> > To: [email protected] > Sent: Monday, September 7, 2009 1:08:15 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] can this be possible ? > > 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
