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caleblareau / mgatk

mgatk: mitochondrial genome analysis toolkit
http://caleblareau.github.io/mgatk
MIT License
98 stars 25 forks source link

can be used for snATAC? #41

Closed AnjaliC4 closed 2 years ago

AnjaliC4 commented 2 years ago

Hi, thanks for the tool! Have you guys tried using mgatk for single-nucleus ATAC-seq? How do you think this would perform for snATAC? I guess assumption would be that mtDNA in snATAC come from mitochondria of the same cell?!

Thanks

caleblareau commented 2 years ago

Hi Anjali,

We’ve tried but never had a successful application unfortunately. By definition, the snATAC strips out the mitochondrial so a) there is very little captured; b) there is non-specific signal as you suggested.

The code will run but I can’t recommend spending very much, if any, time on interpreting the analysis as it is unlikely to be fruitful!