Hi there
I did Miseq to some samples a couple of months ago in a company where they sequenced the V4 region of my samples and I ended up with reads of 250bp
I did the analysis (with a lot of help from this forum, thanks for that) and I was pretty happy with it even if I didnt have that long reads!
It seems however that I cant continue sending my samples to that company and I have to find a new one, which I did
In that new company that I found they say that they use 2 protocols: one that amplifies the V1-V3 region and one that amplifies the V3-V5 region and that the reads they produce are about 570bp!!!
from what I understood (and what they told me) is that they create a longer amplicon and when they assemble afterwards the reads there is only a small overlap
i m a bit reluctant to use a protocol like that but I would also like to hear other people’s opinion
do you think its a good idea? should I go for it? or should I just stick to the protocol with the shorter reads (and better overlap)
Cheers
Panos