Chances and challenges in RNA-Seq analysis

Matthias Scherf, Martin Seifert
Genomatix, Germany

RNAseq is a next generation sequencing based technology that facilitates gene expression detection at a high resolution level. It allows to measure and (semi) quantify RNA levels as well as differential analysis. In addition, structural detection of transcripts and splice variants becomes feasible. This is especially helpful for “non-mainstream genomes” as it enables de-novo transcript assemblies and annotation.
Besides these chances also significant challenges have to be overcome. The most important aspect is the inherent diversity and complexity of RNA species and the multitude of potential transcript and splice variants. In this respect, today’s NGS technologies are mainly limited by the read length. Read length also plays a role for mapping positions with insufficient uniqueness. For RNA analyses the correct measurement of paralogous genes are one example. To address these issues different aspects have to be taken into account:
1. The background transcriptome annotation should be as complete as possible
2. Mapping strategies should take the uniqueness into account
3. Visualization is an integral step for consistency evaluation

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