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
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