Hi QIIME2 community,
I ask for help since I have a very strange situation with my data.
The context: my results came from Illumina of 16S for bacteria communities in soil, I processed this data with QIIME2 and I got similar results when comparing with outputs obtained by the sequencing company that also processed the data in QIIME2.
The problem: for this study, an expert collaborator ran the bioinformatic analysis in Unix (Ubuntu) and we realized that our results are the opposite, in summary, we got the opposite trends for alpha diversity! also, in QIIME2 I got half of the sequences than the collaborator. I thought in wrong labels, but that's not the problem, so, has anyone experienced something like this?
I realized that: 1) I obtained approx. 7000 features after denoising and he got approx. 14000; 2) we got similar trends until the rarefaction, after that the outputs show the opposite results; he rarefies in R, I made all the analysis in QIIME2.
I attach part of my script in case someone wants to check it.
Script_QIIME2_forum.txt (5.4 KB)