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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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Usage with alevin output #13

Closed alexvpickering closed 5 years ago

alexvpickering commented 5 years ago

Hello,

Do you have any advice for usage with alevin output? Thank you

alexvpickering commented 5 years ago

Tried this out with little luck. The problem is that is that it is hard to get salmon alevin to quantify all droplets so that the ambient soup gene expression profile can be estimated. I raised the issue on the salmon github repo https://github.com/COMBINE-lab/salmon/issues/377 but am going to switch to kallisto for the time being as it outputs counts for all droplets by default.