Trimming reads prior to 'quality-filter q-score-joined' command

Hopefully a quick question! I am using paired-end reads following the Deblur pipeline. After quality filtering using the following command,

qiime quality-filter q-score-joined
–i-demux demux-joined.qza
–o-filtered-sequences demux-joined-filtered.qza
–o-filter-stats demux-joined-filter-stats.qza

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!

Good afternoon Jordan,

Welcome to the Qiime 2 forums! :qiime2:

Try this plugin. This gives you lots of ways to trim! :scissors:

btw, here's the full list of available plugins.


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] 

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