mm9.2bit

[H Scott Stadler]

Hi,

I am trying to obtain the complete genome assembly MM9 for analysis of some mouse chip-seq data.  I found the mm9.2bit file on your server.  Is this the complete assembly?  More importantly, I work at a hospital that only has Windows 7 64 bit computers.   What program do you recommend that will run in MS Windows that will facilitate the unpacking of the mm9.2bit files?

 

Thank you,

Scott Stadler

 

 

 

H Scott Stadler Ph.D.

Principle Investigator Shriners Hosptial for Children

Associate Professor Molecular and Medical Genetics

Oregon Health and Science University

3101 SW Sam Jackson Park Road

Portland, OR 97239

503-221-3447

503-221-3451 (fax)

 

[Matthew Speir]

Hi Scott,

Thank you for your question about the mm9.2bit file. You are correct that this 2bit file contains the entire genome. Unfortunately, all of the tools that we provide for unpacking these 2bit files into fasta files are only available for UNIX-based operating systems. You can try downloading the mm9 genome in fasta format: http://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/chromFa.tar.gz. You may run into issues trying to unpack a tar.gz file on Windows 7. If so, you will have to download a third-party tool like 7zip, http://www.7-zip.org/, to unpack the files.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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