You do not need Repeat Masker .out files to run blat. Use the argument -mask=lower if you want to exclude the already masked areas of the target sequence.
If you want to run a blat against the entire genome, simply give the mm9.2bit file as the target sequence (the 'database' argument). You will need a machine with at least 8 Gb of memory to run the entire genome at once. Depending upon how often you need to run blat, it may be better to set up gfServer and use the gfClient to run repeated blat operations. --Hiram ----- Original Message ----- From: "Peng Yu" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Friday, June 18, 2010 8:24:53 AM GMT -08:00 Tijuana / Baja California Subject: Re: [Genome] RepeatMasker .out and file.out file for mm9 On Fri, Jun 18, 2010 at 12:17 AM, Hiram Clawson <[email protected]> wrote: > What is it that you are trying to mask ? The mm9.2bit file > is already masked. I want to mask the regions same as the regions in the genome browser RepeatMaster track. The description on the bigZips URL doesn't say mm9.2bit is masked. mm9.2bit - contains the complete mm9 Mouse Genome in the 2bit format. Just to double check if I understand you correctly. Do you mean that I should just use something like the following command without using the -mask=type option, since mm9.2bit already includes the mask. Or even with mm9.2bit, I still need to use -mask=type? there are multiple .out files in chromOut.tar.gz, would you please show me how to let blat use all of them, if I want to blat against all the chromosomes rather than just one chromosome a time? blat -t=dna -q=dna -tileSize=11 -stepSize=5 -minScore=20 -ooc=11.ooc -out=psl mm9.2bit query.fasta query.psl _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
