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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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Is one negative control useless for this application? #134

Open lowrda opened 1 year ago

lowrda commented 1 year ago

Hi!

I have sequenced milk samples (from rats, small amount) but did not take into account the low-biomass issue when I had them sequenced. This means the company that sequenced them only had 1 negative control. I have 30 samples. Is it even worth trying to use decontam with one negative control sequenced? In the future I will be using 5 or 6, as mentioned in the article.

Thanks so much!

Dana

benjjneb commented 1 year ago

Is it even worth trying to use decontam with one negative control sequenced?

No. Well, decontam-prevalence is not worth using (the approach that relies on negative controls).

If you have DNA concentration measurements you could try decontam-frequency.

lowrda commented 1 year ago

Thanks so much for such a quick response, I'll try and use the DNA concentrations then!