I am wondering about how ASVs get classified in qiime2 and how length variation is accounted for. I am looking at 16S data that I put through the dada2 pipeline. For my study I needed to align the rep seqs and after doing so, I found that several are identical except for length variation at the beginnings and ends of the sequences. For example, in the attached file you can see two ASVs that were classified as being different ASVs, but the sequences are the same except that one sequence is 298 bp and the other is 296 bp due to length variation on the 3' end. Is there a reason these 2 ASVs are "different" aside from the fact that they are different lengths? Is there a way to collapse these ASVs within QIIME2?
Thank you in advance for your help!
16SASVseqalignment.txt (1.5 KB)
Welcome to the forum!
This may have to do with your primer trimming steps. How did you pre-process your sequences before passing them to dada2?
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.