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
