I have a question about the
dada2 trimming. Basically we got our demultiplexed paired-end data from our genomics core who used the 16S Metagenomic Sequencing Library Preparation.
We did a presentation in our data and somebody said that primers are still in the sequence data from our core. Do we have to remove primers before running dada2? I checked the raw fastq file for several files. The forward sequences are always starting with
CCTACGGG and the reverse sequences are always starting with
NACTAC. I do not see they match with the Primers, am I right?
My last question is that how to set the
trim and trunc parameters is appropriate in dada2 to trim the primers like I found above?