Each experimental time point was run on an individual flow cell containing the 3 biological replicates with different barcodes.
We ran 5 replicates (with different sets of seeds for random variables) for each of the experiments.
Two hundred replicates with different random values were generated for each bootstrap, sensitivity and missing value analysis.
The sequences of oligos used in this paper are shown in Additional file 9. Sample M-14 was selected to perform technical replicates with different barcodes.
As previously seen with QTL mapping, adding more genotypes does not necessarily increase resolution, only adding biological replicates with different combinations of genotypes is capable of doing that.
Six of the 32 chosen parameter combinations resulted in a return to the homogeneous equilibrium, and were replaced by three centre points in two replicates with different initial conditions.
Users can also select an additional category called 'fill' for separating bars by colour to achieve a third grouping dimension to compare, for instance, replicates with different numbers of depositions.
We performed preliminary simulations to specify the appropriate priors for each analysis, and ran three replicates with different random seed numbers with burn-in periods of 3,000,000 steps and 50,000,000 steps in chain following burn-in.
