Analysis of ATAC-seq paired-end data can reveal indispensable information on nucleosome packing and positioning, patterns of nucleosome-TF spacing, and TF occupancy simultaneously at genome-wide resolution similar to DNase-FLASH [103]. Analysis is based on the distribution of insert lengths and the positions of insertions after Tn5 transposition within open chromatin of active regulatory elements (Step 15). For TF foot printing (Step 14) our laboratory uses CENTIPEDE [151] (see below), although other footrprinting algorithms are also available [19, 78, 83, 85, 128, 146–149]. For footprinting analysis, cleavage sites have to be adjusted four to five bp upstream or downstream due to the biophysical characteristics of Tn5 transposase, which inserts two adaptors separated by nine bp [102]. It is not known if footprinting detection with ATAC-seq data is factor-dependent or affected by Tn5 cleavage preferences.
