Figure 3.

Outline and principles of bisulfite sequencing data-processing pipelines (see the data supplement for an expanded figure legend and the text for details and abbreviations). (A) Our pipeline begins with raw base call (*.bcl) files from Illumina sequencers. It then generates multiple intermediate files and reports, and ends with output files for use in visualization and analysis procedures. (B) The Bismark alignment procedure performs a series of in silico residue conversions to align bisulfite-converted sample fragments to a reference genome. (C) The Bismark methylation extraction (calling) procedure. CHH = cytosine followed by any two noncytosine bases; DSS = Dispersion Shrinkage for Sequencing.