benjjneb / decontammanuscript Goto Github PK

@benjjneb Hi! I am dealing with data with two sets of negative controls: DNA extraction reagent control and sequencing reagent control. As the DNA extraction was done in 4 batches and the sequencing in 2 batches, I am unable to decide the strategy to carry out the decontamination. I was thinking of identifying the contaminants in two steps (first with DNA extraction controls and then with the sequencing run controls). however, I wish to know if I can do this together? Meaning, defining my samples with DNA extraction batch and sequencing run in my metadata/sample data file and then carrying out the decontamination together.

I would like to know your thoughts on this, thanks!