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cole-trapnell-lab / cicero-release

https://cole-trapnell-lab.github.io/cicero-release/
MIT License
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Running cicero on bulk data #32

Closed amr15 closed 5 years ago

amr15 commented 5 years ago

Hi,

I had a naive question--if I'm trying to run cicero on bulk atac-seq data, should I assign each peak randomly to 100 cells? What is the best way to convert cicero for bulk use?

Best, Anu

hpliner commented 5 years ago

Hi Anu,

Unfortunately Cicero is designed for use with single-cell data, and the algorithm will not work with bulk data. It's possible that you could use it with bulk if you have many many replicates (though I make no promises). Because of the correlation calculations, you won't be able to divide up bulk data in a way that will make Cicero work.

Sorry about that, Hannah