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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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Used rarefided or unrarefided feature-table #112

Open suiweikang opened 2 years ago

suiweikang commented 2 years ago

210 samples were sequencing in my research. And the number of sequencing reads of my sample was varied greatly, from 40,000 to 210,000. Also, the number of sequencing reads was rarefied to 40,000. \ Should rarefied or unrarefied feature-table used in decontam?

benjjneb commented 2 years ago

By default decontam will normalize the data to proportions. And so rarefaction is not recommended, especially if negative controls are included which often have significantly lower read counts.

suiweikang commented 2 years ago

Thanks for the reply. Are both the frequency or prevalance method based on the proportion? Or is frequency based on proportions, while prevalence based on absolute read number?

benjjneb commented 2 years ago

The prevaaece method is based on presence/absence, so a proportion > 0.