Figure 2

Biases of the observed FPKM displayed as density distributions. We visualize the effect of the library (a), alignment (b), and counting biases (c) on the observed FPKM. The log2-ratios were constrained to the range [-2, 2] and the density distributions were generated using a band-width of 0.05. The library composition has the biggest impact and causes over- as well as underrepresentation. The aligners do not align all reads correctly but achieve a very high rate for the majority of the genes. If the transcripts exhibit variable transcription start sites and poly-A tails the alignment rate for the short isoforms drops (see the Additional file 1 for the per isoform mapping rates).