I have found reads in my negative controls (one blank sample from the DNA extraction and a PCR negative control). So I've already denoising my data with DADA2, and I want to export my table.qza and my metadata to R for decontamination of my samples using the package decontam.
I've seen a lot of discussions in the forum about using decontam and I read decontam tutorial. But my main difficulty is how can I insert my table with my ASVs and my metadata correctly for analysis in R.
With my data entered, I understood that I need to follow the identification of contaminants by prevalence.
Here are my files:table-single.qza (212.1 KB)
sample-metadata.tsv (2.0 KB)
Thanks in advance
Did you manage to solve this doubt? I'm stuck on this too.
If you're brazilian too we can help each other in portuguese at the private messages
So, to export your table.qza or any other file from qiime2 to R you can follow the qiime2R tutorial, it will give you the steps to introduce your files in R, here are the github from qiime2R too.
Once you're with your qiime files in R you can follow the tutorial from Decontam. I recommend to look to the number of negative controls that you have in your dataset, because Decontam works well with a certain number of this type of samples.
Another option is to use microDecon, it worked well with my dataset that just have two negative controls (one from extraction and other from PCR). If you need Here are the microDecon tutorial.
Yes, I'm Brazilian!
Thank you so much for your answer. I will see your files recommendations and any questions I call you ate the private messages