Since that combination is not supported by BLAT, swap the target database and query:
blat -t=dnax dna_query.fa -q=prot proteome.fa output.psl -Galt On Wed, Jun 27, 2012 at 12:31 PM, Steve Heitner <[email protected]> wrote: > Hello, Amit. > > > > Since that combination is not supported by BLAT, go ahead and swap the > target database and query as in your original email. > > > > Please contact us again at [email protected] if you have any further > questions. > > > > --- > > Steve Heitner > > UCSC Genome Bioinformatics Group > > > > From: Amit Pande [mailto:[email protected]] > Sent: Wednesday, June 27, 2012 2:05 AM > To: [email protected] > Subject: Re: [Genome] BLAT - six frames > > > > Hello Steve, > > I already tried what you wrote to me but it gives me the following error: > > Loaded 22243362 letters in 51824 sequences > Unrecognized combination of target and query types > > It works if I switch -q with -t, but it wouldn't be correct this > way....would it ? > > warm regards, > Amit. > > > > > > On Tue, Jun 26, 2012 at 10:29 PM, Steve Heitner <[email protected]> > wrote: > > Hello, Amit. > > You were very close. You just need to reverse your database and query > options. The correct command should be: > > blat -t=prot proteome.fa -q=dnax dna_query.fa output.psl > > Please contact us again at [email protected] if you have any further > questions. > > --- > Steve Heitner > UCSC Genome Bioinformatics Group > > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Amit Pande > Sent: Tuesday, June 26, 2012 2:23 AM > To: [email protected] > Subject: [Genome] BLAT - six frames > > Dear Curators, > > I am trying to run BLAT locally on the command line. I have a query file > which consists of DNA and a database file which has proteome. > I am using dnax option because I want the query to be translated in 6 > frames > to protein and then align it to the database. > > The command I am typing is: > > blat proteome.fa dna_query.fa -t=dnax -q=prot output.psl > > I am not sure about the results, kindly tell me whether this is the right > way to execute the program . > > Thank you in advance, > warm regards, > Amit. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
