Tag: Chimeric Transcript

ChiTaH – Chimeric Transcripts from High-throughput sequencing data

ChiTaH

:: DESCRIPTION

ChiTaH is a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data.

::DEVELOPER

Rajesh Detroja

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ChiTaH

:: MORE INFORMATION

Citation

Detroja R, Gorohovski A, Giwa O, Baum G, Frenkel-Morgenstern M.
ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data.
NAR Genom Bioinform. 2021 Nov 26;3(4):lqab112. doi: 10.1093/nargab/lqab112. PMID: 34859212; PMCID: PMC8633610.

EricScript 0.5.5 – Identify Chimeric Transcripts in RNA-seq data

EricScript 0.5.5

:: DESCRIPTION

EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data.

::DEVELOPER

EricScript team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 EricScript

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 15;28(24):3232-9. doi: 10.1093/bioinformatics/bts617. Epub 2012 Oct 23.
Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.
Benelli M, Pescucci C, Marseglia G, Severgnini M, Torricelli F, Magi A.

FusionSeq 0.7.0 – Detect Chimeric Transcripts from Paired-end RNA-seq Experiments

FusionSeq 0.7.0

:: DESCRIPTION

FusionSeq is a computational framework for detecting chimeric transcripts from paired-end RNA-seq experiments. It includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and provides a ranked list of fusion-transcript candidates that can be further evaluated via experimental methods. FusionSeq also contains a module to identify exact sequences at breakpoint junctions.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FusionSeq

:: MORE INFORMATION

Citation:

Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stephane Terry, David Z. Chen, Joel S. Rozowsky, Ashutosh K. Tewari, Naoki Kitabayashi, Benjamin J. Moss, Mark S. Chee, Francesca Demichelis, Mark A. Rubin, Mark B. Gerstein
FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data
Genome Biology 21 Oct. 2010; 11:R104

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