DADA2_Truncating both forward and reverse reads_how?

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

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


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!

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