Fig. 3
Features of gene transcription revealed by alignment of reads in the cDNA libraries. a Relationship between aligned bases (x-axis) and percentages (y-axis) of the genome overlaid with reads using TopHat. Each colored symbol represents one library, with their library IDs labeled (Fig. 1). Squares for paired-end libraries; circles for single-end ones. The dashed lines are linear regression of the data from the paired- and single-end libraries. b Box-plot of percentages of the mapped genome in library categories P (paired-end, 33), S (single-end, 19), H (head, single-end, 8) and A (antenna, single-end, 7) (Fig. 2). c Heatmap of z-scores in each group of base range. BPKM values were used for sorting into 19 groups. Group 1 has the highest BPKM values 1–400; Groups 2 to 19 correspond to BPKMs ranked 401–800, 801–1600, 1601–3200, … 400 × 2n + 1 to 400 × 2n + 1, where n equals 0 to 17. The heatmap is colored based on the z-score of average BPKM in each group. Libraries with black and cyan IDs were determined by paired- and single-end sequencing, respectively. d Percentage of aligned bases for each BPKM group in the total aligned bases for a specific library. The library names and their color codes are described in Fig. 1