FIGURE 5.

Mispriming can cause misinterpretation of RNA polymerase pausing. (A) Sequence logos showing sequence enrichment spanning 20 bp around mispriming sites identified by our pipeline for two published GRO-seq data sets. (B) View of GRO-seq peaks adjacent to sequence matching the 3′ adapter sequence. (C) Heatmap showing pausing index (PI) for 230 genes that show at least twofold difference in PI before and after filtering for mispriming reads. Rows are ordered by decreasing ratio of PI in filtered to PI in unfiltered data set. (D) Heatmap showing distribution of reads proximal to transcription start site and gene body in unfiltered (left) and filtered data set (right) for 230 genes shown in C.