5’ and 3’ ends of mapped sRNAs as well as pooled CAGE 5’ ends were overlaid windows of 601 bp centered on forward strand summits of enhancer-defining CAGE tag clusters and sense strand summits in promoters of RefSeq protein-coding genes. The average cross-correlation between CAGE 5’ ends and sRNA 3’ ends were calculated in these windows allowing a max lag of 300. For footprint plots, reads mapping to the same genomic locations were only counted once not to make any library or genomic region have an undue influence.
