I am doing 16S rRNA gene sequencing on the Illumina MiSeq platform. In several papers, I found that they have targeted different variable regions for this purpose. Although there might not be a concrete answer to this, I want to make sure that I target the best variable region during 16s library preparation. In this case, I am positive about targeting variable region V3-V4. Does anyone have a good suggestion regarding this? Help will be appreciated. Thank you!
Thank you, Dr. Abhijeet Singh. I had researched that primer as well. But, for some reason, many of my fellow mates suggested to use S-D-Bact-0341-b-S-17 by Kindworth et al (2013), IlluminaS-D-Bact-0785-a-A-21 (rev). Hopefully, this will work better.
If you are going to use S-D-Bact-0341-b-S-17 by Kindworth et al (2013), IlluminaS-D-Bact-0785-a-A-21 (rev), then it is better to sequence it as 2x300 for merging paired reads. If only 2x250 option is available, 515F-806R may be a better choice, as advised above.
Best,
Thank you Dr. Timur Yergaliyev for your suggestion. I am doing PE300 for sequencing.
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