Hi @sindhu_mohandas,
No actually, Dada2 will not perform properly if your reads are pre-joined with another tool. The main issue is that this is in conflict with the error-building approach utilized by Dada2. When you join reads you are assigning new quality scores (calculated differently between different tools) in the overlapping region which are not true q-scores which Dada2 uses. So, you want to run raw data without any prior modifications. What you’ve done is more appropriate for Deblur however, as Deblur uses a static error model and does not rely on quality scores.
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