Question: where to download mm9.fa masked?
0
gravatar for Michel Edwar
10 months ago by
Michel Edwar70
Sweden
Michel Edwar70 wrote:

Hello,

I wonder if someone can direct me to a website, where I can download the mouse genome (9) masked for repeated regions.I think the UCSC website have masked files by chromosome, but not the whole fasta file.

Thanks

chip-seq genome • 438 views
ADD COMMENTlink modified 10 months ago by simon.vanheeringen200 • written 10 months ago by Michel Edwar70
6

cat ?

ADD REPLYlink written 10 months ago by Pierre Lindenbaum129k
4

No, mouse!

ADD REPLYlink written 10 months ago by WouterDeCoster44k

lol :) funny Thanks, I will try it.

ADD REPLYlink written 10 months ago by Michel Edwar70
0
gravatar for Jean-Karim Heriche
10 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

You can get this from the Ensembl FTP site. Since this is an old version, you'll have to figure out which release to you want to use, e.g. URL for release 60: ftp://ftp.ensembl.org/pub/release-60/fasta/mus_musculus/dna/

EDIT: Just realized that Ensembl actually doesn't have genomes in one file. I thought they had because I have used such a file before but I must also have used cat on the individual chromosome files.

ADD COMMENTlink modified 10 months ago • written 10 months ago by Jean-Karim Heriche23k
0
gravatar for simon.vanheeringen
10 months ago by
simon.vanheeringen200 wrote:

Using genomepy this is straightforward*:

genomepy install mm9 UCSC -m hard

*Disclaimer: I would say so, as I'm the author ;-)

ADD COMMENTlink written 10 months ago by simon.vanheeringen200

You may want to consider creating a single tools post for your software. See examples under tools tag for inspiration.

ADD REPLYlink written 10 months ago by genomax87k
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