We are planning to work on microbioma analysis by NGS with MiSeq.
Have you any experience on working with the primers selected by Illumina for their protocol?
How about the purification by using AMPure XP Beads? Any other option?
Thank you,
Andrea
Hi Andrea.
I know that it wouldn't be the best answer, but the best way is to contact with your sequencing facility in the case you contract their services. They can tell you which contidions are the best for you.
Hi Felipe,
The thing is that I will sequence my samples, so I would like to know if somebody have any experience with the Illumina protocol.
Thank you for your help.
Andrea
Whether they will work for you depends on how you want to use the data. They will produce good sequence for the V3-V4 variable regions with no more bias than most primer sets; if that is sufficient for your needs then you should not have any problems.
You can test the 16S-specific part of the primers at https://www.arb-silva.de/search/testprime/ and get an idea whether specific taxa you want to have included will likely be properly amplified.
Tim
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