The goal of this analysis is to determine if the experiment was successful and is often performed by constructing composite plots and by visualization (Steps 4, 6, 9, and 12). Multiple tools are available for generating composite plots including ArchTEX [108], DANPOS-profile [109], and CEAS [110]. For example, TSSs have been shown to be chromatin accessible on average across all eukaryotic genomes [48, 111, 112]. A drop of composite plot signal intensity is expected at this feature when analyzing MNase-seq data, whereas DNase-seq, FAIRE-seq and ATAC-seq data will exhibit an overall increase at the same sites. ArchTEX can also be used to assess the cross-correlation of MNase-seq data, with successful experiments exhibiting enrichment at nucleosomal banding sizes [113]. ATAC-seq QC can be further performed by estimating the percentage of sequence reads that map to the mitochondrial genome and by generating ‘insert size metric plots’ using Picard tools. High quality ATAC-seq data will coincide with a low percentage of mitochondrial reads, and a distribution of insert sizes that depicts a five to six nucleosomal array along with ten bp periodicity of insert sizes.
