Scientists at Tsinghua University, China have used the negative binomial (NB) distribution to model sequencing reads on exons, and propose a NB-statistic to detect differentially spliced genes between two groups of samples by comparing read counts on all exons. The method opens a new exon-based approach instead of isoform-based approach for the task. It does not require information about isoform composition, nor need the estimation of isoform expression. Experiments on simulated data and real RNA-seq data of human kidney and liver samples illustrated the method’s good performance and applicability. It can also detect previously unknown alternative splicing events, and highlight exons that are most likely differentially spliced between the compared samples.
DSGseq is available at http://bioinfo.au.tsinghua.edu.cn/software/DSGseq.
- Wang W, Qin Z, Feng Z, Wang X, Zhang X. (2012) Identifying differentially spliced genes from two groups of RNA-seq samples. Gene [Epub ahead of print]. [abstract]