We have recently performed analysis on a gut microbiome dataset (16S) where we used QIIME 1.9.1 to demultiplex pooled Illumina sequence reads (earth microbiome project protocol) and split reads per sample (split_libraries_fastq.py; split_sequence_file_on_sample_ids.py), rarefy our OTU table (single_rarefaction.py), and calculate UniFrac distances (beta_diversity.py). We will be moving to QIIME2 for future analyses, but we are now wondering if we need to go back and reanalyze using QIIME2.
Is this necessary? Are there any differences between QIIME 1.9.1 and QIIME 2 we need to be aware of in these areas?
We also have a replication dataset yet to be analyzed, so we want to use QIIME 1.9.1 on this dataset as well for consistency with the previously analyzed dataset.
Any help will be most appreciated!