DADA2_Truncating both forward and reverse reads_how?

[Kruttika_Phalnikar]

Dear qiime community,

I am running dada2 for denoising my data

My qual visualization plots look like this

I run the follwing command

qiime dada2 denoise-single
--i-demultiplexed-seqs demux.qza
--p-trim-left 0
--p-trunc-len ()
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza

now my forward reads are better than reverse and can be truncated after 245 position
Reverse reads can be truncated after 190 position
But I just have 1 option to put truncation value?
If I put 190, do I lose good amount from forward reads?
Is like I can't truncate both forward and reverse reads separately?

I tried using --p-trunc-len-f and --p-trunc-len-r
qiime says it can't recognize these commands

I am refering to this discussion

Truncating parameters on DADA2 (paired-end demultiplexed reads)

Hi, I am working with paired end reads that have been demultiplexed but have not undergone any other processing by the sequencing company (so primers/adapters are still attached). I imported using Phred33 manifest file. The graphs of the unjoined sequences are below: [screenshot] [R1R2] Based on this comment, I ran the following DADA2 command, using a smaller truncation parameter for the reverse reads based on the graph (Do I need to remove the primers/adapters first? I did not... I see fro…

in dada2 original tutorial, there is an option of truncating f and r separately before merging.

Could someone please explain?
Thank you so much in advance

Kruttika

[Nicholas_Bokulich]

Hi @Kruttika_Phalnikar,
The issue is that you are using qiime dada2 denoise-single, but you should be using qiime dada2 denoise-paired. Check the help docs — that method has the --p-trunc-len-f and --p-trunc-len-r parameters that you are looking for.

I hope that helps!