I have got paired-end Illumina (2 x 300) dataset for 16S. I use qiime 2 demux summarize commands. The company has provided me with clean data with no primers or barcodes. Then I use DADA2 denoising by using the following commands
qiime dada2 denoise-paired **
–i-demultiplexed-seqs demux.qza **
–p-trim-left-f 6 **
–p-trim-left-r 6 **
–p-trunc-len-f 300 **
–p-trunc-len-r 300 **
–o-table table.qza **
–o-representative-sequences rep-seqs.qza **
However, the sequence counts in Table. qzv were very low as compared to demux.qzv. The data demux.qzv and Table.qzv is attached to this message.
Please explain to me why the sequence counts are reducing in Table. qzv ? Am I doing any mistake? I would be thankful if you guide me.