How the cut-site probability is calculated?

[crazyhottommy]

Hi, I am reading https://bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.html and for the TF footprint figure, how the y-axis cut-site probability is calculated?

Is it the average read counts for each base pair (100 bp flanking the motif) and then the average count of each base pair across all the motif occurrence was calculated? How this value is normalized?

Thanks, Ming

[jianhong]

The counts number is calculated by the 5' ends or fragment center depend on your setting. Default is the 5' ends. And normalized by the factor of library size/coverage size.