Bias correction within transcripts. An example showing the effect of bias correction on the read counts for human transcript NM_004684. The top panel shows raw read counts (number of 3' ends of fragments at each location), and the bottom panel shows the product of the bias parameters (total bias weight defined in the Supplementary methods in Additional file 3) at the same locations. We correctly identify bias at different positions and can therefore correct for the non-uniformity. Note that the bias parameters were learned from the entire dataset excluding reads mapped to this transcript in order to cross-validate our results. The RNA-Seq for the experiment was performed with the NSR protocol , which is why 3' counts were used instead of 5'.