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How to get mouse genomes to test CNV tools with?

Hi, I'm currently working on an internship to develop a cnv detection tool, and at the current stage I need to test 4 CNV calling tools that I have selected (cnvnator, control-freec, cnvkit and amplicone).

I'm trying them out with mouse genomes, since I'm ultimately working with those in the long term, and I've already got my reference genome (GRCm39).

However, I'm slightly confused about how to acquire the "test" data. I don't have any real sequencing data to work with yet, so I was trying to get it somewhere online. I've heard the Mouse Genomes Project may have something like that, but I think I'm stuck with the reference data for each strain they've sequenced.

Is there anything I'm missing? I feel that I'm being silly here, but up until now I've only worked with reference genomes or with already sequenced data that was directly given to me, so I'm unfamiliar with this process.

cnv grcm39 genome mouse cnvtools
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written by Pipschroma • Pipschroma

1 answer

You can download genomes and fastq data here

  • NCBI genome/datasets
  • ensembl
  • EBI ENA for fastq data
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written by colindaven colindaven

Actually, I found out I misinterpreted what kind of data I need, seems I'm looking for BAM files after all. Forgot to say, but I've gone through those databases as well and wasn't finding anything, guess I understand why now.

Thank you for answering though!

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written by Pipschroma • Pipschroma

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