Branch-seq accurately identifies BP locations on a genome-wide scale. (A) Schematic of the Branch-seq protocol. Steps labeled with “B” and “L” correspond to Branch-seq and Lariat-seq, respectively. (B) Branch-seq locates the annotated 5′SS (pink) and BP (blue) in the PCH2 intron (Sureau 2001; Wollerton et al. 2004; Robinson et al. 2011). Dashed lines show locations of 5′SS (GTATGT), BP (CACTAAC), and 3′SS (AG) sequences. Mismatches from consensus are underlined. BP nucleotide is red and bold. Mismatches in reads are indicated by small red, green, dark blue, and orange horizontal lines. Inset axes show read start locations for PCH2 intron 5′SS and BP reads where the 0 nt is the 5′SS or BP nucleotide, respectively. (C) Meta 5′SS and BP read start plots as in B but for all annotated 5′SS and BPs. Dotted vertical lines at ±2 nt. (D) Locations of BP peaks called by winBP and GEM-BP relative to annotated BP positions.
