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Where can I find mouse BAM files?

Hello, I'm working on a CNV project and I've reached a step where I'm in need of some mouse BAM files to test CNV tools with.

Thing is, as far as I can tell, the only files that are available through databanks are only compatible with mm38. Is there anywhere I can find mm39 BAM files? Or do I have to do the mapping for them myself? Please tell me if I haven't been clear enough.

Thanks!

cnv grcm39 genome mouse mm39
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updated by Matthias Zepper Matthias Zepper • written by Pipschroma • Pipschroma

Why don't you find papers that benchmark CNV tools and use their data? Yes, you might need to remap to mm39 as the genome is relatively recent.

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written by ATpoint ATpoint

SRA has a quite advanced search logic. A maximally restrictive query could look approximately like this:

("Mus musculus"[Organism] AND "wgs"[Strategy] AND "filetype bam"[Properties]) AND ("illumina"[Platform]) OR "oxford nanopore"[Platform]) OR "pacbio smrt"[Platform] OR "element"[Platform]) AND ("mm39"[All Fields] OR "GRCm39"[All Fields] OR "GCF_000001635.27"[All Fields])

It indeed doesn't find anything yet, but you can try expanding your search my tweaking the query to what is tolerable for your purpose. Is there a specific reason why you need mm39 specifically?

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written by Matthias Zepper Matthias Zepper

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