negative controls metabarcoing pipeline

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Hi everyone,

I am new to bioinformatics and I am currently processing my eDNA data with my pipeline. I have split the reads from my actual samples from the reads of negative controls because otherwise, no data would be left for the negative controls. I am wondering if this is the right way to go. On one hand, I want to filter out the noise but I also want to keep some of the sequecing data from my negative controls so that I can use decontam. But I am wondering what the best way is to go about this. Does anybody have some tips?

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Welcome to the forums! :qiime2:

Can you share with us the command you used to do this? There are many ways to do this, so knowing the exact command is helpful.

In case you have not found these already, here are the two decontam tutorials?

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