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download mm9 mouse genome fasta file

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

sequencing chip-seq
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updated by Denise CS Denise CS • written by mikysyc2016 mikysyc2016

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

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written by ATpoint ATpoint

2 answers

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.

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written by Alex Reynolds Alex Reynolds

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.

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written by Denise CS Denise CS

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