Why does Illumina recommend running a control phiX sample in one lane of each flow cell?
The data from the control sample are used to generate the matrix file. The analysis tool uses the control to calculate phasing/pre-phasing from this sample, and the relative proportion of the different bases. Without a control lane, the software would assume that the base composition of the sample is strictly balanced. While this is true of a total human genome, it might not be true of non-human genomes or a focused region of the human genome. Therefore, the control is necessary for all expression studies, small RNA studies, and reduced complexity studies.