Method for Producing Genome Signal Track

Cited from the paper "Cooperative Binding of Transcription Factors Orchestrates Reprogramming"

Genome signal tracks of features (TFs, histone marks, ATAC-seq and RNA-seq) were calculated by partitioning the genome into non-overlapping bins of fixed size (100b for TFs, ATAC-seq and RNA-seq, and 25bp for the histone marks). RPKM values were calculated for each bin using the number of sequencing reads that overlap with the corresponding bin. For histone marks, each read was extended by 200 bp in the direction of the alignment.