~90% of reads removed when denoising using DADA2 (V1V3 REGION)

Hi all.

I have run the following script to find that ~90% of my reads have been removed. my data is run on the V1V3 region (27F, 519R):

qiime dada2 denoise-paired
--i-demultiplexed-seqs manifestout.qza
--o-table dada2-table.qzv
--o-representative-sequences dada2.qza
--o-denoising-stats stats.log
--p-trim-left-f 20
--p-trim-left-r 20
--p-trunc-len-f 280
--p-trunc-len-r 260 stats.log.qza (7.8 KB)

--p-n-threads 0

my stats.log file showed me the following reads:

sample-id input filtered denoised merged nonchimeric
#q2:types numeric numeric numeric numeric numeric
cootharaba 298145 219309 219309 36137 26068
elandapoint 475098 350153 350153 73133 47619
marycairncross 325176 246113 246113 38025 23889
palmercoolumresort 438216 318817 318817 107108 75149
twinwaters 172007 114811 114811 20359 13407
usc-BPHLF 254296 185189 185189 22404 18021

Our worry is that this loss of reads will display a bias within the community results. I have been told this is common of the V1V3 region.
Would the forum recommend that parameters be further optimised, or should the forward read be analysed only?

My end result for this project is to compare multiple variable regions (3).

Thanks in advance for your help.

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