p-min-quality for joined reads

[amaria.gallego (Adriana)]

Cordial greeting.

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

[colinbrislawn (Colin J Brislawn)]

Hello Adriana,

Take a look at the full documentation for that plugin: q-score-joined: Quality filter based on joined sequence quality scores. — QIIME 2 2020.2.0 documentation

Looks like the --p-quality-window is three by default, and those dips in quality are at single locations. Have you tried setting the windows to 1?

Colin