Picking OTU's with samples generated by different primers
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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
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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.

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