srnaMapper: an optimal mapping tool for sRNA-Seq reads

Abstract

MotivationSequencing is the key method to study the impact of short RNAs, which include micro RNAs, tRNA-derived RNAs, and piwi-interacting RNA, among other. The first step to make use of these reads is to map them to a genome. Existing mapping tools have been developed for the long RNAs in mind, and, so far, no tool has been conceived for short RNAs. However, short RNAs have several distinctive features which make them different from messenger RNAs: they are shorter (not greater than 200bp), they often redundant, they can be produced by duplicated loci, and they may be edited at their ends. ResultsIn this work, we present a new tool, srnaMapper, that maps these reads with all these objectives in mind. We show on two data sets that srnaMapper is more efficient considering computation time and edition error handling: it quickly retrieves all the hits, with arbitrary number of errors. AvailabilitysrnaMapper source code is available at https://github.com/mzytnicki/srnaMapper. Contactmatthias.zytnicki@inrae.fr