Question: Picking OTU's with samples generated by different primers
gravatar for nathalimachadolima
4.2 years ago by
nathalimachadolima10 wrote:

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 • 953 views
ADD COMMENTlink written 4.2 years ago by nathalimachadolima10

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.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Bioinformatics_NewComer320
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