Somewhat embarrassed to ask this, but just cant figure out how to do it. So the table.qzv that you get after the dada2 processing of reads lists the actual ASVs and their overall distribution across the entire dataset (i.e. in the feature detail you can find each ASVs’s frequency and the # of samples it is present in, but thats it). Is there a way to generate a table with the detailed distribution: ASV1 is present x times in sample a, y times in sample b, ASV2 is present… in sample … Not just overall statistics? Went through some convoluted old posts and explanations but no clear answers. I would think the info all is available in the DADA2 that is not part of the actual output file? This is not related to phylogenetic classification, rarefaction, alpha diversity, none of that, simple question, ASV frequency across each sample. I actually need to analyze some SNPs in an amplicon dataset not in a phylogenetic or diversity framework. Can one get that in QIIME2, or should run DADA on the outside? Thanks
The base information you’re looking for is the table.qza artifact. The sequences are in the representative sequence file. You. can export the data to R using qiime2R or you can export and manipulate in a different format to your hearts delight.
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.