download mm9 mouse genome fasta file

Question

[mikysyc2016]

Hi all, I start to analysis the ChIP-seq data, but first i need mm9 mouse genome fasta file. How you get it from Website? If you know how to , can you introduce some details? Thanks in advance! Yachen

[ATpoint]

Any reason why you use mm9 and not the recent mm10? If you start a new project, you better go with the current mm10.

Answer 1

[Alex Reynolds]

UCSC Goldenpath is a good resource: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/

From that site's README:

Using an rsync command to download the entire directory:

rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/ .

These are gzipped files. So you'll need to run gunzip on each of them after downloading them locally.

Answer 2

[Denise CS]

Download mm9 (aka NCBIm37) from the Ensembl FTP. You will have both the repeat masked and not masked sequences. Check their README for all the details.