I have a paired-end fastq WGS sample, and I want to extract the 16s rRNA for the downstream analysis. I have googled and some people recommend SortMeRna for implementation. And I found this tool in QIIME2 page.
But I didn't find the tutorial for this function, could someone provide some examples on how to run this one?
I have already imported my data and generate my qza file using " Fastq manifest".
Thanks in advance, this forum has been enormously helpful to me!
Thanks for reaching out! We actually don't currently have any tools within QIIME 2 for 16S region extraction from WGS data. The core QIIME 2 distribution is primarily used for marker gene studies vs. WGS or shotgun analysis.
I did a quick search on 16S region extraction from WGS data, and there may be a couple of tools for you to look into on this discussion board. I haven't looked into any of them in depth, but this sounds like it may lead you in the right direction. Best of luck!