Hypervariable region

The analysis given in the MothurSOP used silva V4 for the alignment , while in my own microbiome research we used V3-V4 region. Can I still use the V4 for the alignment?

No, the V4-based instructions in the SOP only cover the V4 region. If you want the alignment coordinates for the V3-V4 regions, you’ll need to do some extra work…

Sir, kindly guide on how to go about it. I am using V3-V4 region for my study.