Problems with dada2 clipping and denoising

Dear Qiime developers,
When I run dada2 with the following code in the terminal, something was wrong. I want to leave the 0-195 fragments and cut off the bases after 195. However, when visualizing rep-seq.qzv, the intercepted fragments are not correct.

time qiime dada2 denoise-paired
–i-demultiplexed-seqs paired-end-demux.qza
–p-trim-left-f 0
–p-trim-left-r 0
–p-trunc-len-f 195
–p-trunc-len-r 195
–o-table table.qza
–o-representative-sequences rep-seqs.qza
–o-denoising-stats dada2-stats.qza \

Do you have any idea how to solve this issue ?

Thanks a ton

1 Like


By providing this command, you are trimming your forward and reverse reads to the length 195. So they are trimmed by Dada2, and then merged, since you have paired reads. Different pairs of reads have different overlapping region, so in the output you are receiving sequences that are different in size and bigger than 195 (non-overlapping part of R1 + overlapping region + non-overlapping part of R2).
So, there is nothing wrong with the command you are running.