I’m analyzing V3-V4 amplicon data (Illumina 150 bp or 300 bp paired-end) from 16S rDNA loci and used deblur to denoise the raw data (after qiime quality-filter q-score).
In the deblur script it is stated that “Only forward reads are supported at this time”. Does this mean that the reverse reads are ignored (like analyzing only 150 bp single end data)?
I realized that deblur returns more ‘representative_sequences’ compared to DADA2, which tries to join paired-end sequences (which can be difficult if the overlap is not good enough). Even 300 bp paire-end data sets are often not ‘true’ 300 bp, because the quality tents to drop above 200 bp and should be truncated by --p-trunc-len-f and --p-trunc-len-r, respectively .
So, does it make sense to use deblur on paired-end reads, if only the forward strand is used?
Is there an option not to loose non-joined sequences after DADA2 step for subsequent analyses?