Does anyone have the experience of using Nimblegen exome seq kit or customized seq kit to enrich their samples before sequencing the DNA?
My question is how many samples could we multiplex per capture reaction? Clearly the answer depends on the desired coverage depth, and I am also aware that capture is not homogeneous so some regions may get more covered/captured than others. Moreover, the coverage depth will certainly increase if we sequence the capture product multiple times/lanes. But I was wondering what people's general experiences are with these kits when they multiplex the samples.
e.g. When we capture one sample per capture reaction, what's the expected/estimated coverage depth on average for one run sequencing in one sequencing lane (HiSeq)? When we multiplex 2 samples per capture reaction, what's the expected/estimated coverage depth on average? When we multiplex 8 samples per capture reaction, what's the expected/estimated coverage depth on average?
Any info sharing will be greatly appreciated !!
To clarify - The kit comes in different sizes - 4 rxn, 12 rxn, 24 rxn ..etc. Ideally, each rxn is for one sample capture. However, I assume the oligos in the rxn are in EXCESS, so in principle, we should be able to pool 2-3 (or more) samples per capture and still get enough read depth of sequence for each sample. I was wondering if people have done it and if so, what's recommended and not-recommended for multiplexing in the capture reaction.