RT Journal Article
SR Electronic
T1 CLAN: the CrossLinked reads ANalyais tool
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 233841
DO 10.1101/233841
A1 Cuncong Zhong
A1 Shaojie Zhang
YR 2017
UL http://biorxiv.org/content/early/2017/12/14/233841.abstract
AB 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.