I am working on a 16s rRNA data.
The raw data consists of roughly 30 samples and
each sample has its forward and reverse FASTQ files.
When I import the data, I used a manifest file
with “PairedEndFastqManifestPhred33” option,
so that I can make one “output.qza”.
Now, I could see the quality plots for the forward and reverse parts
to decide how much I can truncate in the DADA2 procedure.
At this point, I feel a bit confused because this pair of quality plots are about all the samples.
That is, I could get the pair of quality plots from each sample individually.
The quality plots for each sample might show a different tendency,
implying I have to use distinct truncations for each sample.
I am sorry if this is duplicated thread but
I was wondering whether my bundling-up approach is still okay.
Thank you for reading any input would be very appreciated.