On Fri, Jun 18, 2010 at 10:24 AM, Peng Yu <[email protected]> wrote: > 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
I just check the format of .2bit, and the following page says it include the mask information. Therefore, I can just use the above command without any -mask options supplied, right? http://genome.ucsc.edu/FAQ/FAQformat.html#format7 >> You can get the RM .out files from this directory: >> >> http://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/ >> >> --Hiram >> >> ----- Original Message ----- >> From: "Peng Yu" <[email protected]> >> To: [email protected] >> Sent: Thursday, June 17, 2010 7:45:18 PM GMT -08:00 Tijuana / Baja California >> Subject: [Genome] RepeatMasker .out and file.out file for mm9 >> >> Hi, >> >> blat has -mask option which can take these 2 values. I'd rather not to >> install RepeatMasker for now due to some license issue. Since there is >> a RepeatMasker track in the genome browser, there might be some >> RepeatMasker output file publicly available. Would you please let me >> where to download these two files for mm9 if they are available >> somewhere? >> >> out - mask according to database.out RepeatMasker .out file >> file.out - mask database according to RepeatMasker file.out >> >> -- >> Regards, >> Peng >> > > > > -- > Regards, > Peng > -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
