Hi,
I have pacbio hifi reads data (whole 16S gene amplified) and I ran it through Karken2 pipeline with green genes database using Partek flow software and I also ran the same dataset using QIIME2-DADA2-green genes database as described in Analyzing PacBio HiFi Mock Community 16S Data with QIIME 2 · PacificBiosciences/pb-16S-nf Wiki · GitHub
The issue is that both outputs are showing exact opposite alpha diversity. Kraken pipeline shows that Shannon Index is significantly higher in Control vs. KO, whereas QIIME2-DADA2 output shows that Shannon Index is lower in Control vs. KO. Usually two different approaches never show contrasting trends. Significance might alter but not trend.
I need guidance in deciding which output is more reliable for publishing.
Please guide me in figuring this out.
Best,
R