Hi @Mehrbod_Estaki,
Many thanks for the feedback. Is working now and I have obtained the table-without-chloroplast and other filters.
To optimize I am wondering If I can clean up multiple (contaminants) in one line? I tried: –p-where “Taxon NOT LIKE ‘%Chloroplast,Mitocondria%’” but it just recognize Chloroplast, not mito. Any suggestion? Or do I have to filter again the table-without-chloroplast and do several filters in each new table?
What I am trying to do is find if the ASV are exclusive of a specific group so then I can sum the samples, and then merge the runs (3), should I use my new tables without contaminants for this?
Can the ASV be a mutation or variant of another ASV? Is this define in Dada2 step or the ASV will be obtained even if there is just 1 bp difference?
As I am working in barcoding, I am interested in finding the unique or exclusive ASV per sample and then group. In my understanding, if the ASV is not present in the duplicate sample, therefore, is a PCR error or mutation. How could I compare the samples as an initial filter instead of having to do beta diversity per sample as the last step of the pipeline? I was following your other comment (Filtering for private ASVs - #3 by Nicholas_Bokulich) in the forum about (core-features combining different tables), is there any example or notebook that you could share?
-p-min-fraction FLOAT (the ASV in one sample? )
--p-max-fraction FLOAT ?
Also, I would like to extract the ASV that are in each sample so I can have a table with (features/samples and add an abundance of the feature in the sample), any thoughts?
Many thanks and bests,