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benjjneb / decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
https://benjjneb.github.io/decontam/
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Cell-line negative controls #81

Open chrisquatjr opened 4 years ago

chrisquatjr commented 4 years ago

Hello, first of all thank you for putting this package together. My lab is doing some metagenomics analysis on biological RNA-Sequencing samples and the only negative controls we have are cell line controls. More specifically, on each of our sequencing plates, we have a control well that is typically filled with an aliquot of jurkat cells, which is our approximation of a water control. I read that this package is designed with water controls in mind, but is there a way that I can use cell-line negative controls instead with this package? I would be happy to provide further details or additional clarification if needed. Thank you for your time.

benjjneb commented 4 years ago

The conceptual assumption is that the negative controls should not legitimately have any "true sample" DNA/RNA in them. That is, the DNA/RNA that is the actual biological signal in the real samples should be absent (except for contamination) in the negative control samples. So, if this control sample type meets that conceptual assumption, then the decontam approach should work in principle.

chrisquatjr commented 4 years ago

Got it! Thank you for the info.