Dada2: Losing reads at merging step

Hi @Mehrbod_Estaki

Thanks for replying to my previous post (Dada2: losing reads during merging the topic got closed because I took too long to reply, so am starting a new topic).

I appreciate your response but I am unsure if it is correct. You said:

With your primer set we would expect an amplicon size of 926-515= ~414 bps.

I thought that this was the amplicon size before removing primers. However, in my case I already removed the primers with cutadapt. Moreover, when I remove primers with cutadapt and then merge reads with vsearch, most of the merged reads have between 370-375 bp. This is consistent with my understanding that the amplicon length is without primers, because ~414bps - 39bps=~375 (my primers are 19 and 20 bps).

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