Interpretation of demux file.qzv for trimming and truncating

I am a new user of QIIME and I have read through the forum posts but still not confident with my understanding. I am currently trying to decipher the demux-paired end qzv file.
invertspairend-demux.qzv (289.7 KB)

And this is how I have interpreted it based on the plot above. Is this correct?

qiime dada2 denoise-paired
--i-demultiplexed-seqs ./invertsdemuxpairend-demux.qza
--p-trunc-len-f 162
--p-trunc-len-r 120
--p-trim-left-f 10
--p-trim-left-r 10
--o-representative-sequences xx-rep-seqs-dada2.qza
--o-table xx-table-dada2.qza
--o-denoising-stats xx-stats-dada2.qza
--p-n-threads 10

Many thanks,

It all depends on how long your actual amplicons are. The read pairs must be long enough to join if you want to use both pairs!

Unless if that is enough for your reads to join, try:

–p-trunc-len-f 200
–p-trunc-len-r 180 

But long story short: try and see what works. See the xx-stats-dada2.qza file to make sure you are not losing too many reads at the filtering or merging (joining) steps.

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Hi Nicholas,
Thank you for such an informative reply, it is quite clear now as I proceed to the next step. The length of the amplicon that I am trying to filter/merge is 563bp.

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