I have next figure (see below) and I want to remove those reads with quality lower than 25. I used next code
qiime quality-filter q-score-joined --i-demux joinedreads-end-demux.qza --p-min-quality 25 --o-filtered-sequences demux-joined-filtered.qza --o-filter-stats demux-joined-filter-stats.qza
I checked the results before and after applied the command and they look similar (see below the figure)
the matter is related with the p-min quality number? can I use 25? does it should a specfic number, I mean 20 or 30?
Thanks a lot