1> Hello, I use qiime feature-table summarize (default setting) to check my feature table (ASVs). I don’t think the output is what I need. Is this possible to to give me a summary something like QIIME 1 OTU table. For example, I have 3 samples and 100 unqiue ASV. I want to something like this
sample 1 sample 2 sample 3
feature 1 10 20 4
feature 2 3 4 5
2>Also, how does people normally rarefy feature table in Qiime 2 (just switch from qiime 1). For example, I have 3 samples. The number of reads of each sample is 10,000, 20,000, 30,000.
I know qiime feature-table rarefy, but this seems to do different thing? I am really confused here. I don’t think the frequency in the feature table means the number of the reads? It’s just the feature counts.
3> Where can I find my reads/persamle information after I build the feature table. The only file that I can see this is after my reads/persample is after I multiplexer? However, after this step, I can’t see anything about reads/persample, even I run dada workflow. If I want to rarefy to equal number of reads across samples, I should do it before DADA workflow? – Or rarefy by equal sequencing depth has been updated?
4> I guess the point here is that is how can I track the sequence/persample after build a feature table. As my experience, I run Dada workflow and build a feature table. I did multiple filtering (e.g., filter ASVs that I don’t want or low abundance ASV). Eventually, I have an feature table that I am going to do some serious analyses and I would like to do equal-depth subsample and want to know the number of reads of the final feature table. Also, I don’t think I need to do any filtering for rep_seqs or raw seqs according to the tutorials. The rep_seqs and raw req files are almost never used.
frequency in the feature table (ASV) = number of reads or not?