combining analysis of reads of different V regions (V3, V4)


I am stuck on my data analysis dealing with MiSeq reads from different V regions. How can I combine these dataset into a single pipeline (or is it possible to do so and at what stage/step in mothur pipeline)?


If you have different regions, then you need to do separate analyses and see if they agree with each other. In general, I discourage doing separate regions.


To build on this question… I encountered a dataset with V3-V4 amplicons that have been sequenced with 2x150bp. The only way to analyze this would be to analyze read1 and read2 separately, no? Because in some papers I’ve seen an approach where they include a linker sequence with Ns if the reads don’t overlap (e.g., though these would get filtered out in mothur anyway.

RIght. Using the Ns in the middle is pretty… not smart.