I got a recent issue while running two similar paths but only changing dada2/deblur from the same sample groups.
From sample group 1,2 and 3 i ran dada2 or deblur following commands below (as suggested in q2 tutorials). For deblur i ran:
qiime quality-filter q-score
–o-filter-stats deblur_files/demux-filter-stats.qza ;
qiime deblur denoise-16S
And for dada2 (I did this 3 times, for each group as they came from 3 separate sequencing runs followed by a table and rep-seqs merge).
qiime dada2 denoise-paired
For both options I followed the same downstream analysis to alpha diversity metrics Observed OTUs and Chao index, and observed significant changes whether the denoising followed (just an example with Chao, but is the same situation with observed OTUs). Group 2 (in the middle) is changing a lot its richness, as well as its p value compared to other groups. In the image (up is Chao index computed from deblur files, and down from dada2 files)
On the other hand, when estimating alpha diversity with Shannon index (taking into account evenness) the situation is the same in both cases, so there’s no problem.
I also checked both denoising stats and saw that samples from groups 1 and 3 had more reads after deblur than dada2(as I suppose it’s normal), but group 2 samples had more reads after dada2 than deblur (don’t know if could cause changes).
Any idea about what could be going on? I hope everything is clearly explained!
Thanks a lot for your support!