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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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DNA concentration inputs #116

Open devinjones18 opened 1 year ago

devinjones18 commented 1 year ago

Hi Ben,

This is probably a dumb question... Does it matter which stage before sequencing we use DNA concentrations for 'decontam'? For example, should I use the DNA concentration of the extract itself? Or the normalized DNA concentration from the step immediately prior to sequencing (post-pcr and addition of index tags, etc)?

Thanks, Devin

benjjneb commented 1 year ago

We've found DNA concentrations measured at different steps in the process can work. The key thing though is that these DNA concentrations must be taken before the "normalization" of the libraries to try to get equal numbers of reads in each sample.