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?
Welcome to the forum @Wilming!
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.
Thanks a lot! It helps me