The rep_seqs and raw req files are almost never used.įrequency in the feature table (ASV) = number of reads or not? Also, I don’t think I need to do any filtering for rep_seqs or raw seqs according to the tutorials. 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. I did multiple filtering (e.g., filter ASVs that I don’t want or low abundance ASV). As my experience, I run Dada workflow and build a feature table.
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?Ĥ> I guess the point here is that is how can I track the sequence/persample after build a 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. I don’t think the frequency in the feature table means the number of the reads? It’s just the feature counts.ģ> Where can I find my reads/persamle information after I build the feature table. I know qiime feature-table rarefy, but this seems to do different thing? I am really confused here. I want to something like thisĢ>Also, how does people normally rarefy feature table in Qiime 2 (just switch from qiime 1). For example, I have 3 samples and 100 unqiue ASV. Is this possible to to give me a summary something like QIIME 1 OTU table. 1> Hello, I use qiime feature-table summarize (default setting) to check my feature table (ASVs).
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