Overall, most initial data analysis steps are the same for all chromatin accessibility assays discussed above and are normally done by the NGS facility performing the sequencing reactions. These steps include demultiplexing, alignment to a reference genome, tag filtering and measurement of sequencing quality control (QC) (Figure 2). The goal of this stage of analysis is to determine if the sequencing was done with the required depth of coverage and to prepare BAM alignment files for downstream assay-specific analyses.
