Hi, i have been struggling with dada2, using qiime2. I have 2*250 bp (paired-end reads) covering the V3-V4 regions using 341F and 806R primers. My quality plots are:
My problem is that i am losing a lot of data in the merging step.
I used the following command:
qiime dada2 denoise-paired \
(first i used in trunc-len-f 192 and trunc-len-r 198, but the loss was huge, and so a tried the above insted) .
This was my results:
Do you think that i should change my parameters? Thanks