Following trimming, my forward and reverse reads seem to be very high quality except for at two positions (25 and 143) in the middle of the forward read:
So for the DADA denoising step I ran the following command without truncation. Will the max error parameter most likely resolve the two base pairs (25 and 143) that are lower quality? Or should I probably use --p-trunc-q 20 or 30 to get rid of reads with lower quality data?
qiime dada2 denoise-paired
--verbose &> DADA2_denoising.log
Additionally, I noticed the min length of my representative sequences is 95 when the amplicon size is normally ~390 bp. Is this normal or should I try to filter out the shorter sequences? It seems my reads are good lengths so I am not sure why they would be merging to form reads that are so short?