merge quality-filter q-score-joined sequences

I have paired end reads from multiple Miseq runs. Samples are different for each run but library and sequence targets are same 16s V3-V4. I used vsearch to merged R1 and R2 for each run. I want to try another workflow aside DADA2.

Is it possible to merge quality-filter q-score-joined sequences from the different runs and then denoise the merged sequences by deblur?

Hi @prince,

Have you checked out the Alternative Methods of Read Joining tutorial? I (generally) find that the tutorials cover like 85-90% of my pipeline questions.



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