CLAN: the CrossLinked reads ANalysis tool

Abstract

The crosslinked RNA sequencing technology ligates interacting RNA strands followed by next-generation sequencing. Mapping of the resulting duplex reads allows for functional inference of the corresponding intramolecular/intermolecular RNA-RNA interactions. However, duplex read mapping remains computationally challenging, and the existing best-performing software fails to map a significant portion of the duplex reads. To address this challenge, we develop a novel algorithm for duplex read mapping, called CrossLinked reads ANalysis tool (CLAN). CLAN demonstrates drastically improved sensitivity and high alignment accuracy when applied to real crosslinked RNA sequencing data. CLAN is implemented in GNU C++, and is freely available from http://sourceforge.net/projects/clan-mapping.