low non chimera output

[oluwatobi (oluwatobi Emmanuel fijabi)]

Am running 16S analysis for V4 region of drosophila microbiome and getting low non chimera between 40-50%. Could someone help out. Although I discovered that my reverse reads were bad

qiime dada2 denoise-paired
--i-demultiplexed-seqs demux-paired-end.qza
--p-trim-left-f 5
--p-trunc-len-f 249
--p-trim-left-r 4
--p-trunc-len-r 165
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza
--o-denoising-stats stats-dada2.qza
stats-dada2.qzv (1.2 MB)

[jphagen (Johannah Hagen)]

Hi @oluwatobi,
I would suggest searching the forum for different ways other users have dealt with low chimeric output. Considering the low quality of your reverse reads, that should be taken into account when adjusting any parameters. This post has some helpful tips on dealing with low output after chimeric filtering.
--Hannah