qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trunc-len-f 250 --p-trunc-len-r 240 --p-trim-left-f 20 --p-trim-left-r 19 --p-trunc-q 2 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --output-dir dada2-dmx-pe_data.qzv
This command i run and i got only 34% merging. will that be ok to further process and analyse . as most of the reads got filtered out