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 “align_seqs.py -h”, How should I proceed further to calculate the relative abundance of OTUs across the experimental and control samples.

Thanks

@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 https://docs.qiime2.org in order to get familiar with QIIME 2. In the meantime, we are here to help with any specific questions. Welcome to the community!

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