Searching how to improve my taxonomic results in forum I have found this topic that is something like our proceeding. We amplified full 16S gene, randomly fragmented at 150pb and sequenced by MiSeq Illumina platform. After that, Illumina BaseSpace suite is used to primer and barcode trimming and demultiplexing. Initially, we proceed with "Moving Pictures tutorial" pipeline with some changes like
dada2-paired instead of
dada2-single or the addition of
orient-seqs. Our taxonomic results don't fit with the expected abundances (we use a mock community to check that) although the observed bacterial genres are what they should be.
Now, I read that DADA2 is not capable of processing this kind of reads because of DADA2 presumptions. How should we proceed? In the topic linked above it is suggested to merge R1 and R2 files but I am not sure how this is done. How do you get the
Feature Table and the
Representative sequences files?
On the other hand, for shotgun analysis, some forum topics recommends to use
q2-metaphlan2 to do the taxonomic classification but if we are interested in explore alpha diversity, we need the pre-processing step to obtain
Feature Table and
What procedures should we follow to analyze our samples? Do you have any other suggestions?