I looked through some similar posts and could not find exactly what I was looking for in regards to DADA2 truncation length and trimming of V4 region reads.
Study includes environmental controls( expecting low reads) and clinical samples
V4 region only sequenced, using 806r and 515f primers
overall observe median good quality with reverse showing high variation throughout sequence length.
unlike V3-V4 or other regions in this dataset I do not see a distinct cutoff and was wanting others opinions or insights.
I am thinking potentially:
--p-trunc-len-f 130 --p-trunc-len-r 135 --p-trim-left-f 0 --p-trim-left-r 10
CPPdemux.qzv (324.4 KB)