Merged files, where should I start in the pipeline and how?

[seqlt]

I have the .fastq files for the F and R sequences that were processed and merged but would like to test if I will get the same results as the one I did with the dada2 pipeline but cannot figure it out how can I add these merged files into the pipeline

Thank you so much

[benjjneb]

We do not recommend pre-merging sequences, as it can interfere with the DADA2 error model.

But you can move forward with the tutorial workflow as normal, just skip the reverse read and mergePairs step and run makeSequenceTable(dadaFs,...) instead of makeSequenceTable(mergers,...).

[seqlt]

Thank you so much