dada2 merging and comparing different data sets

[colinbrislawn (Colin J Brislawn)]

Hello Alya,

Welcome to the forums! Sorry to keep you waiting on an answer. It's been quite the February!

@Alya_Heirali

Is it appropriate to compare the two data sets given these differences?

Yes! See this great discussion on GitHub about processing data from multiple runs.

@Alya_Heirali

I tried cutting the ROMA2 reads to 142,140 to make them more comparable but had difficulties merging my forward and reverse reads.

As long as the region sequenced is the same after merging, you can pick the truncLen settings that work best for your data! See this comment from the dev:

It's fine to use different truncLen parameters as long as the read pairs still overlap and are mergable at the end. The truncLen setting doesn't affect the merged amplicon region, it just affects the amount of overlap between the two reads.

I think the method you describe here should work great!

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@Alya_Heirali

Is it appropriate to merge ASVs belonging to the same species?

That's a good question. I think the consensus on the Qiime 2 forums is to keep your ASVs separate for most downstream analysis so that you can make use of their subspecies resolution. However, it could be convenient to talk about 'species' instead of 'ASVs of the species' in the discussion section, and I like to merge features by taxonomy when I make stacked bar plots. Your call!

Let us know if you have any other questions!
Colin

P.S.

@Alya_Heirali

Any thoughts/tips would be much appreciated.

Microbiome Datasets Are Compositional: And This Is Not Optional