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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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Can i use "frequency" without DNA concentration? #144

Closed kx11jkjk closed 8 months ago

kx11jkjk commented 9 months ago

Hello, thank you for your team's contribution to decontamination. I found some microbial cohort from the public database, but there is no negative control or DNA concentration information, is there any way to use your method for decontamination? In the OTU table, rows are samples and columns are microbes. I am considering caculating the sum of each row to replace DNA concentration information for 'frequency' method. Is this method feasible? If it doesn't work, is there a better way? Thanks for your help! Here is my data looks like: OTU1 OTU2 OTU3 sample1 0 3 1 sample2 2 5 45 sample3 1 0 0

kx11jkjk commented 9 months ago

Snipaste_2024-03-04_00-48-49

benjjneb commented 8 months ago

but there is no negative control or DNA concentration information, is there any way to use your method for decontamination?

No.

I am considering caculating the sum of each row to replace DNA concentration information for 'frequency' method. Is this method feasible?

No. Read counts don't reflect input DNA concentrations, because libraries are mixed in varying ratios to try to get the same number of reads per sample.

kx11jkjk commented 8 months ago

thank you！