Confusion about ' --p-trunc-len-f '

[Wilming]

In the code below:
time qiime dada2 denoise-paired
--i-demultiplexed-seqs trimmed-seqs.qza
--p-trim-left-f 35
--p-trunc-len-f 220 \

I want to know -- does p-trunc-len-f 220 mean to cut to the position 220(from 35 to 220), or does it mean to cut from 35 to 255 in a 220 length area?

[Nicholas_Bokulich]

Welcome to the forum @Wilming!

@Wilming

I want to know – does p-trunc-len-f 220 mean to cut to the position 220(from 35 to 220), or does it mean to cut from 35 to 255 in a 220 length area?

Good question. It means the position, not the length. As the help docs says:

Position at which forward read sequences should be truncated due to decrease in quality.

So in effect the trim and truncation parameters operate independently of one another.

[Wilming]

Thanks a lot! It helps me