Picking OTU's with samples generated by different primers
Entering edit mode
6.2 years ago

Hello, I need to analyse differents data to do biodiversity comparison, and I have data generated using bacteria general primers and sample using cianobacterial primers. I would know how can I pick OTU's if I have differents regions of 16S?

Thank you!

qiime next-gen • 1.2k views
Entering edit mode

May be you should have different mapping file for each region, and then carry out further analysis? For that one should have proper sync with lab-technician to provide samples which fall under which region.

Also, my understanding is, a particular parameter might not work all the same with different region. E.g.: Quality for V4 might not be applicable for V3-V4 region, and, or vice-versa.

Does that mean the pipeline has to be run end-to-end for each region separately?

I'd love to hear some solution here. I've recently stumbled onto this: multiple regions sequenced in one gigantic raw file. Thanks.


Login before adding your answer.

Traffic: 1294 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6