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
> 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
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