From Genome Technology Core (GTC) wiki - Sequencing and Microarray
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Unbalanced samples typically come from methylation sequencing, small RNA sequencing, ChIP sequencing, or sequencing of genomes with a high or low GC content. Experiments and samples that need a control lane are listed in Table below. In general, most DNA and RNA sequencing experiments of mammalian genomes do not need a separate control lane for corrections, though a control lane could be used for troubleshooting purposes and as a quality reference point. If you want to run a number of samples and you are not sure whether to use a control lane, perform a run with a control lane and compare analysis with and without the control lane. Based on that, you can decide whether to use a control lane for subsequent similar experiments.

Controllane solexa.JPG