Plots for Figure 4 E

[khayer]

Could you please comment on which output file you used to create figure 4e? Similarly can NucleoATAC be used to create Figure 3 C from Buenrostro et al. 2013?

Thanks in advance

[AliciaSchep]

The output file was the nucleoatac_signal.bedgraph.gz output. The supplement shows heatmaps at the TSS for both the nucleoatac_signal and the occupancy (Supplementary Figure 16).

Sure it could be used to create something like Figure 3C. You could potentially make a coverage track (using pyatac cov) and then multiply by the occupancy track (to get a level of nucleosome coverage) and by (1 - occupancy track) to get a level of nfr coverage.