title: Janus--a comprehensive tool investigating the two faces of transcription.
abstract: BACKGROUND
  Protocols to generate strand-specific transcriptomes with next-generation sequencing platforms have been used by the scientific community roughly since 2008. Strand-specific reads allow for detection of antisense events and a higher resolution of expression profiles enabling extension of current transcript annotations. However, applications making use of this strandedness information are still scarce.
  
  
  RESULTS
  Here we present a tool (Janus), which focuses on the identification of transcriptional active regions in antisense orientation to known and novel transcribed elements of the genome. Janus can compare the antisense events of multiple samples and assigns scores to identify mutual expression of either transcript in a sense/antisense pair, which could hint to regulatory mechanisms. Janus is able to make use of single-nucleotide variant (SNV) and methylation data, if available, and reports the sense to antisense ratio of regions in the vicinity of the identified genetic and epigenetic variation. Janus interrogates positions of heterozygous SNVs to identify strand-specific allelic imbalance.
  
  
  BACKGROUND
  Janus is written in C/C++ and freely available at http://www.ikmb.uni-kiel.de/janus/janus.html under terms of GNU General Public License, for both, Linux and Windows 64×. Although the binaries will work without additional downloads, the software depends on bamtools (https://github.com/pezmaster31/bamtools) for compilation. A detailed tutorial section is included in the first section of the supplemental material and included as brief readme.txt in the tutorial archive.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany. m.barann@mucosa.de
authors.forename: Matthias
authors.initials: M
authors.lastname: Barann
authors.forename: Daniela
authors.initials: D
authors.lastname: Esser
authors.forename: Ulrich C
authors.initials: UC
authors.lastname: Klostermeier
authors.forename: Tuuli
authors.initials: T
authors.lastname: Lappalainen
authors.forename: Anne
authors.initials: A
authors.lastname: Luzius
authors.forename: Jan W P
authors.initials: JW
authors.lastname: Kuiper
authors.forename: Ole
authors.initials: O
authors.lastname: Ammerpohl
authors.forename: Inga
authors.initials: I
authors.lastname: Vater
authors.forename: Reiner
authors.initials: R
authors.lastname: Siebert
authors.forename: Vyacheslav
authors.initials: V
authors.lastname: Amstislavskiy
authors.forename: Ralf
authors.initials: R
authors.lastname: Sudbrak
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
authors.forename: Philip
authors.initials: P
authors.lastname: Rosenstiel
mesh_terms: D002461:Cell Line, Transformed; D019175:DNA Methylation; D020869:Gene Expression Profiling; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016372:RNA, Antisense / Q000096:biosynthesis*; D012984:Software
chemical_list: D016372:RNA, Antisense