where to download mm9.fa masked?

Question

[Michel Edwar]

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

[Pierre Lindenbaum]

cat ?

[WouterDeCoster]

No, mouse!

[Michel Edwar]

lol :) funny Thanks, I will try it.

Answer 1

[Jean-Karim Heriche]

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.

Answer 2

[simon.vanheeringen]

Using genomepy this is straightforward*:

genomepy install mm9 UCSC -m hard

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

[GenoMax]

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