Complete Bam Files For The Mouse Genome

Question

[Assa Yeroslaviz]

Hi,

I am looking for complete bam files for the mouse genome, similar to the 1000genome project ftp site. Does anyone has a clue as to where can I find this kind of experiments.

I am not really interested in doing the mapping again, unless there is no other choice, but I would like to know if there is some kind of a data base/archive, where people upload his kind of data.

Thanks Assa

Answer 1

[David Quigley]

Which mouse genome did you want? You have your choice at the Sanger's Mouse Genome page. This is the starting point for mouse genomes. You can pull down mapped BAMs for C57BL/6 (the reference genome) or a variety of other strains. You can also pull their raw reads if you later decide to re-map. I think their data are hosted at the European Nucleotide Archive, answering the "where is the data uploaded" question.

Note that their reads were aligned with MAQ; if you prefer another aligner, you'll need to re-map from the raw reads.

[Assa Yeroslaviz]

Is there a way to pull down many files at one time?

[David Quigley]

The BAMs are sitting on an FTP site. Connect with a FTP client and pull down everything you need. Just stay within the terms of service of the site (don't try to simultaneously download the entire database all at once).

Answer 2

[Larry_Parnell]

Perhaps the Strains, SNPs and Polymorphisms page at MGI will link you to the info you need. Of the various items and data available, these look good:

Inbred Strains of Mice.[?] - Characteristics of Inbred Strains of Mice and Rats by M. Festing[?] - View lists of Official Mouse Strain Names[?]

Search for SNPs by strain(s), SNP attributes, genomic position, or associated genes.[?] - SNP Query

[Assa Yeroslaviz]

Am I wrong, or is this only lists of names and breeds. I need the raw/mapped data. I couldn't find it here. I know the site and already search it, but couldn't find any real data. It would be nice f you can pinpoint me to it.