Professor Peter Stadler
Bioinformatics Leipzig, Germany
J Schell seminar room
UGent-VIB Research Building FSVM
9052 Zwijnaarde (Gent)
High-throughput RNA-seq data have become an abundant and cost-effective source of data. Their analysis, at least in model systems with available reference genomes, entails (1) read mapping and (2) reconstruction of transcripts from the mapped reads. Both steps involve -- often tacit -- assumptions on the transcript structure. In particular, it is typically assumed in prokaryotic systems that transcripts are uninterrupted, co-linear intervals on the genome. In Eukaryotes one has to allow for splicing, but co-linearity is still enforced in most analysis pipelines. Reads and trancripts that violate these assumptions are removed from further analysis.
Recent discoveries of circularized RNAs with regulatory functions, however, demonstrated that the assumption that we already know what we are supposed to find is often unwarranted and precludes the discoveries by design. In my presentation I will focus on unusual and unexpected RNAs and the necessary modificiations in computational tools to inspect the contents of the "RNA-seq trash bin".