Systematic bias. Integrated Genome Browser display of chromosome 1 showing four window read count tracks derived from Johnson et al.'s NRSF H. sapiens ChIP-Seq data (A). The datasets were sub sampled to contain matching number of reads and the number of reads falling within a sliding 100 bp window plotted across each chromosome. Both the unamplified and amplified control input datasets show both obvious and subtle regions with an above random number of mapped reads. Expanded views of the input data track pericentric heterochromatic regions on chromosomes 1 (B) and 7 (C) along with UCSC's RepeatMasker tracks show that satellite (red) repeats overlap some but not all regions of apparent mapped sequence enrichment. This systematic bias is also apparent within genes and at transcription start sites (D). The degree of bias varies by dataset. For example, figure E, derived from Valouev et al.'s GABP ChIP-Seq data, shows very pronounced transcription start site read enrichment in the control input and chIP sample.
Nix et al. BMC Bioinformatics 2008 9:523 doi:10.1186/1471-2105-9-523