I’m losing about half my reads per sample. My quality for the first and last 20 nucleotides is very poor, and I thought trimming those regions could help retain a higher number of reads. So far I haven’t found a way to do this in qiime2, and hoped someone might point me in the right direction. Thanks!
Hi @jrede,
Lots of options with cutadapt post-hoc as @colinbrislawn mentioned, but in the future you can also use the trim/truncate options directly in deblur while you are denoising.
--p-trim-length INTEGER
Sequence trim length, specify -1 to disable
trimming. [required]
--p-left-trim-len INTEGER
Range(0, None) Sequence trimming from the 5' end. A value of 0 will
disable this trim. [default: 0]