How to calculate relative abundance of OTU after OTU clustering through 16s RNA reads

I have a dataset with 29 experimental and 82 control samples of paired-end reads, Using SortMeRna I have extracted out the 16s reads. Now I want to cluster these reads against the representative OTU, and further want to calculate the relative abundance of the OTUs.

I have converted the 16s fastq reads to a fasta file and processed through “ -h”, How should I proceed further to calculate the relative abundance of OTUs across the experimental and control samples.


@jaz - it sounds like you were running QIIME 1 up until now - are you looking for help with QIIME 2 at this point?

@thermokarst Hi, I have installed QIIME-2 recently and trying to learn the commands, unfortunately, sometimes it happens that you stuck in a situation where you don’t get enough time to read sufficient content. I installed Qiime-2 Yesterday and have to present my data this week thats why I was looking for a quick guidance and posted this Question, but thank you for your suggestion and response. I am trying to understand the workflow through QIIME 2 help content.

Well, sounds like you have your answer there! You will need to spend some time reviewing in order to get familiar with QIIME 2. In the meantime, we are here to help with any specific questions. Welcome to the community!

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.