Examples of TSSs associated with different classes of RNA. All the corresponding genes are shown left to right regardless of whether they are encoded on the forward (A), (B), (C) and (D) or the reverse (E) strand. The global RNA-seq data for genes on the forward and reverse strand is coloured black and red, respectively. Furthermore, reads corresponding to the reverse strand have been given negative values. (A), (B), (C), (D) and (E) show data corresponding to monocistronic mRNAs (PPA001, PPA002 and PPA004), polycistronic mRNA (PPA0134-6), ribosomal RNA (PPA2417-2419), transfer RNA (AlaCGC) and sRNA (tmRNA), respectively. The panels are screenshots from the UCSC Microbial Genome Browser . In each panel the tracks depict from top to bottom, the position of annotated genes (protein or RNA coding, as appropriate), the positions of TSSs identified by the analysis of M-A scatterplots (Additional file 3), and the number of times each position on the corresponding strand was sequenced following fragmentation of the transcriptome (gRNA-seq). The numbers at the ends of the RNA-seq tracks indicate the scale of the sequencing reads, while the numbers at the top of each panel indicate the genome position. TSSs in black text were judged by viewing of the gRNA-seq data to be clearly associated with leading edges of transcription, while those in blue text were not. EN indicates that a TSS was en riched following TAP treatment.