Quality filtering while merging (not recommended)
paired read merging
The fastq_mergepairs command supports quality
filtering by expected errors. The maximum number of expected errors is
specified by the
fastq_merge_maxee option, e.g.:
SampleA_R1.fastq -fastqout merged.fq -fastq_merge_maxee 1.0
The number of expected error is a floating-point number. Using 1.0 specifies
that the merged read should have zero as the most probable number of errors
according to its Q scores.
Not recommended for making an OTU table
If you are going
to create an OTU table, you should perform quality filtering as a separate
step using the fastq_filter command.
This is because many reads with >1 expected errors will map successfully to
an OTU so you will get better sensitivity by mapping all reads.
Therefore, the best strategy is to perform
OTU clustering or denoising
(error-correction) with quality-filtered reads then
create the OTU table (otutab command) using all
merged reads before quality filtering.