I'm tring to locate some sequences in my rep_seq file after dada2 and relate them with their corresponding sample ID...
Specifically, I'm analysing the effect of the addition of some strains in soil samples... thus, I want to locate the sequences from my strains in the samples. Analyzing the rep_seqqza file after dada2, I can see the sequences and the number of samples they can be found in. However, I cannot know what are those samples... and for me it is very important if they are located in treated soils or control ones... I already locate the sequences by downloading the fasta file... but I don't know what are the samples where they were detected.
Great! and how can obtain this kind of results? I mean, I already have both FeatureTables (after dada2 you got rep. sequences and frequency table), and also the metadata table... but I don't know how to get the table I need... just a table similar to the Frequency Table but with all the samples and the number of times I got each sequence in each sample...
First, we run qiime dada2 denoise-single ... --o-table ./dada2_table.qza,
and later we run qiime feature-table summarize ... --o-visualization ./dada2_table.qzv
That is the output of feature-table summarize, which is a .qzv file.
Go back a step to the output of dada2 denoise-single, which is a .qza file. Export the contents of that file and open it up with a text editor. Inside there is the table we are looking for.