csRNA-seq accurately captures stable and unstable sites of transcription initiation sites from total RNA. (A) Chromatin states of csRNA-seq TSS clusters in human K562 cells as determined by ChromHMM. (B) Comparison of csRNA-seq TSS with other genome-wide assays at the PIM1 locus. (C) Example of an unstable TSS cluster from a gene-distal regulatory element at single-nucleotide resolution. (D) Comparison of read depths at TSS clusters determined by csRNA-seq and GRO-cap (Core et al. 2014) in K562 cells.