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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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microbiome decontamination #99

Open antoine4ucsd opened 3 years ago

antoine4ucsd commented 3 years ago

Hello I am looking for advices for the best way to clean up microbiome sequencing data that have been contaminated by Mock community (Zymo) controls. I know how many cells to retrieve per species per sample but I am not sure how to filter out these cell/species for a given list of samples.

see attached an example of estimated number of cell to retrieve from the pseq object by sample and species. any thoughts?

thank you !

Zymo mock community contaminants.csv

benjjneb commented 3 years ago

If you know the ASVs (or OTUs or taxa) in the Zymo control, you can just remove those taxa from the table. This is done using basic R commands if working with dada2-style sequence tables, or with package-specific filtering commands if using phyloseq for example.

antoine4ucsd commented 3 years ago

Agree. No need to make it complicated. Thank you

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On Aug 6, 2021, at 6:39 PM, Benjamin Callahan @.***> wrote:

 If you know the ASVs (or OTUs or taxa) in the Zymo control, you can just remove those taxa from the table. This is done using basic R commands if working with dada2-style sequence tables, or with package-specific filtering commands if using phyloseq for example.

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