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. 2011 Oct 15;27(20):2903-4.
doi: 10.1093/bioinformatics/btr467. Epub 2011 Aug 11.

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

Matthew K Iyer  1 , Arul M Chinnaiyan, Christopher A Maher
Affiliations

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

Matthew K Iyer et al. Bioinformatics. .

Abstract

Summary: Next generation sequencing (NGS) technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts in high-throughput transcriptome sequencing data.

Availability: http://chimerascan.googlecode.com

Contact: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
ChimeraScan flowchart. (A) Paired-end reads failing an initial alignment step are segmented and realigned to detect discordant reads. Discordant reads that pass filter criteria are realigned across putative chimeric junctions. (B) Chimera with encompassing (blue) and spanning (red) segments detected during realignment.
See this image and copyright information in PMC

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