For each input file of the analysis, the ChIP-Seq Analysis tool calculates and reports several quality measures. Those quality measures have been investigated by the modENCODE consortium and are described in more detail in [Landt et al., 2012]. The quality measures are:
- Number of mapped reads
- For mammalian cells (e.g. human and mouse), this value should be at least 10 million reads. For smaller organisms such as worm and fly, this value should be at least 2 million reads.
- Normalized strand coefficient
- The normalized strand coefficient describes the ratio between the fragment-length peak and the background cross-correlation values. This value should be greater than 1.05 for ChIP-seq experiments.
- Relative strand correlation
- The relative strand correlation describes the ratio between the fragment-length peak and the read-length peak in the cross-correlation plot. This value should be high (at least 0.8) for transcription factor binding sites, which have a concentrated signal. However, this value can be low even for successful ChIP-seq experiments on histone modifications [Landt et al., 2012].