NGS Analysis: From raw reads to biological interpretation.

smallRNA-Seq – Small RNA expression and novel microRNAs


To detect known small RNAs, Genomatix has developed an approach to map reads to our small RNA library without the need for prior linker removal. Usually linker removal is needed, since small RNAs are in most cases shorter than the sequenced read length. For instance, microRNAs are about 21-23 bps long. The Genomatix mapper automatically detects these linkers and removes them, this approach works even without knowledge of the linker sequence. Our small RNA library is a comprehensive compilation from sources like mirBase, Rfam and snoRNAbase.


For predicting novel microRNAs we provide the package miRDeep (Friedländer et al. Nature Biotechnology 2008). First all reads are mapped to the genome to obtain all unique and multiple hits. For microRNAs multiple hits are often biologically relevant, since they can occur in multiple copies in the genome. After mapping the reads miRDeep predicts novel microRNAs and generates an extensive report.


The role of small RNAs is being elucidated in many recent publications. These publications can help shed light on the effect of differentially expressed small RNAs. We provide tools to extract relevant publications that allow linking microRNAs to genes, tissues or diseases. In addition, our pathway tool (GePS) can be used to generate microRNA networks, for instance, interconnecting them with transcription factors.