I did qiime1 and qiime2 analysis on a same dataset and the taxa barplot outcomes of each methods were very different. Qiime2 denoise step had filtered out almost every sequence from 5 of my 17 samples, while qiime1 didn’t seem to have filtered to such extent.
Quality check results to show that the same data has been used:
fastqc Per base sequence quality used for qiime1
qiime2 demux.qzv file
Below is my qiime2 denoising-stats.qzv:
Below are the stats after the filtering from qiime1
- The filtering steps I did after otu picking step in qiime1 include:
parallel_identify_chimeric_seqs.py (ChimeraSlayer), filter_fasta.py (filtered out chimeric seqs), filter_alignment.py (filtered highly variable regions).
Looking at denoising-stats.qzv, a huge chunk was removed after the ‘filtered’ step whereas no such dramatic filtering in qiime1.
Did I skip this step in qiime1 or is this just due to differences in OTU picking and Denoising methods?