Hello,
Thanks for the replies!
I should have shown the reads qualities:
I have done dada2 analysis with multiple parameters.
"With primer" = without use of cutadapt but with trim parameters like "trim 18nt on R1 and 21nt on R2" (so this is normally without primers after the trimming)
Without primer = with cutadapt (~sort of trim 18nt on R1 and 21nt on R2) then trunc 225 (so trunc of 243 on the untrimmed reads):
Results:
We can see an expected loss in the merging step between "With primers with a trunc of 250" versus "with primers with a trunc of 237". But I don't understand why without primers (with cutadapt or a trim of 18nt R1 /21nt R2) permit to have a higher merging results. I can understand why the trim impact the merging step but why the firsts nucleotides are involved in the merging step? I think mainly between these two analysis the orange "With primers : trim 12 & trunc 250" vs the black "With primers : Trim 18/21 & trunc 250", there is a loss of ~7000 reads out of ~35 500 reads, why? For information, the merging reads have a length of about 430 nt.
I have read Looking for help joining paired-end reads - #12 by SoilRotifer but the parameter trim is not involved like in my results right?
Have a good day and thanks again for the assistance.
Jérémy