Paired end: 2x151 vs 2x250 for V4

[SoilRotifer (Mike Robeson)]

Hi all, the decision of whether or not to use 2x150 or 2x250 depends on your sequencing protocol.

For more details on this see the following post:

Trimming and joining short reads resulted in few merged read on v4 region

Hi @simon, If you are indeed sequencing via a 2x150 kit with the EMP V4 (515f-806r primers), and those primers are actually contained within the reads… then sadly these reads will either be to short, or not have enough enough high-quality bases, for merging. The 2x150 sequencing approach works best when using the sequencing strategy outlined here, and the references therein. That is, when using a 2x150 for the V4 region, the sequencing strategy used should NOT sequence through the primers. Mea…

It looks like the EMP web site is not currently accessible, so checkout the protocols.io version.