How do I run the snakemake for mm10 genome?

markowetzlab / scDNAseq-workflow

calling absolute copy numbers on single cell DNA sequencing data - stagging repo for public release

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How do I run the snakemake for mm10 genome? #6

Closed Urja25 closed 9 months ago

Urja25 commented 1 year ago

Hi,

I am trying to figure out how to use the snakemake for mouse data? Any hints on which file I must change?

Best, Urja

leachim commented 1 year ago

@AustinReed-1 can you help with this?

AustinReed-1 commented 12 months ago

Hi @Urja25,

Thanks for your interest!

I have just made a couple changes on the 6-snakemake-for-mm10-genome branch and you should be able to run your mouse data easily now. You only needing to specify the species and genome inputs of the config.yaml file as "Mouse" and "GRCm38" and run as the README file instructs over your mice samples!

Hopefully that helps, Austin