Are abudance tables from different runs comparable?


I am currently doing some analysis of the abundance tables I got from different runs and a question came to my mind... Are abundance tables comparable between them? Or should I repeat the qiime2 analysis with the samples of both runs?

I mean, if I have 10 samples sequenced in the same run and analyze in qiime2 and another 10 samples in another run and analyzed with other dada2 parameters, are the abundance tables comparable? Or should I collect the samples' .fastq files and do the qiime2 taxonomic analysis all together with the same parameters?

Thank you so much in advanced :slight_smile:

Ideally, both runs should be processed with the same version of Qiime2. Each run should be treated separately but with identical parameters, and after denoising (identical parameters!) with Dada2 resulted files can be merged in one table for the analysis.
So, I would take a raw data and process both datasets in parallel with the same parameters until Dada2 and then merge output files to perform taxonomy classification and further analysis.


An off-topic reply has been split into a new topic: Combine subsets of samples from different runs

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