Qiime2 trimming after join-pairs

[Morena_Cau]

Goodmorning all!

My question is:

I done the qiime vsearch join-pairs \ command to join my forward and reverse reads (produced by Miseq) and this is the result.

Which criteria should I use to trim it?
Do I have to use the command:
qiime dada2 denoise-paired
--i-demultiplexed-seqs demux.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 220
--p-trunc-len-r 200
--o-representative-sequences rep-seqs-dada2.qza
--o-table pet-table.qza
--p-n-threads 24

Thank you

[jwdebelius (Justine Debelius)]

Hi @Morena_Cau,

You can’t run dada2 on pre-joined reads. If you want to denoise pre-joined reads, you should use Deblur. Dada2 does all the processing of the reads and requires raw, noisy, unjoined data.

In this case, I think I would either denoise on your forward reads alone, or trim the in the range of 350.

Best,
Justine