Interpretation of demux file.qzv for trimming and truncating

[Imee19]

Hi,
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,
Imee

[Nicholas_Bokulich]

@Imee19,
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!

@Imee19

–p-trunc-len-f 162
–p-trunc-len-r 120

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.

[Imee19]

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.