CCMB Summer Seminar
"Self-training Algorithm for Splice Junction Detection Using RNA-seq"
Jian Ma, Department of Bioengineering, University of Illinois at Urbana-Champaign
Thursday, August 16, 2012 at 11:00 A.M.
Room 241, Swig Boardroom (CIT 2nd Floor)
RNA-seq has proven to be a powerful technique for transcriptome profiling based on next-generation sequencing (NGS) technologies. However, due to the short length of NGS reads, it is challenging to accurately map RNA-seq reads to splice junctions (SJs), which is a critically important step in the analysis of alternative splicing (AS) and isoform construction. In this presentation, I will introduce a new method that we recently developed, called TrueSight. Both simulations and real data evaluations showed that TrueSight achieved higher sensitivity and specificity than other methods. We applied TrueSight to discover novel splice forms in honey bee transcriptomes and found that 65% of honey bee multi-exon genes are alternatively spliced. Utilizing new high coverage transcriptome profiling data and gene models improved by TrueSight, our quantitative analysis revealed that the expression ratio of the splice variants of a single gene is significantly correlated with various genomic features. We believe this new tool will be highly useful to comprehensively study the biology of alternative splicing.