On Fri, Jun 18, 2010 at 10:34 AM, Hiram Clawson <[email protected]> wrote: > 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.
I know that I can run blat without Repeat Masker. But I want to mask the repeat regions. > 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. I'm still confused. If I need RepeatMasker, no matter whether mm9.bit is the database argument or a list.txt file (which includes the path to all the chromosome fasta files) is, I will get the masked results as long as I use -mask=lower option, right? All I need is the blat psl output. The query fasta files in total have a few hundred short sequences (30nt - 75nt). Visualization of a number of matches on the browser is a secondary thing. Therefore, I don't see a clear a reason why my application need gfServer and gfClient. Would you please let me know what type of applications need gfServer and gfClient? > --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 > -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
