Counts were generated for each gene with htseq-count (v0.6.1p1), implemented in the "intersection-strict" overlap mode.
The read counts were generated using htseq-count version 0.5.3p9.
Counts were generated per transcript for each sample.
Transcript counts were generated by summing read counts across all exons of a given transcript.
Counts were generated using htseq-count v.0.5.3p9 with the default "union" overlapping mode.
For SNPs in class k, B i and C i are generated according to the probabilities in V k and W k. ● Next, the observed read counts are generated based on the AS configurations specified by B i s and C i s.
The Audic-Claverie statistics [ 59] are based on a distribution p y | x) over read counts y in one sample in one given group informed by the read counts x under the null hypothesis that the read counts are generated identically and independently from an unknown Poisson distribution.
Gene-level read count was generated using HTseq-count56 and FPKM value was calculated based on the transcript models in GENCODE v19.
Absolute number of read counts and base counts are shown.
Normalised counts plots were generated using ggplot2 version 1.0.0.
