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TrueSight | An algorithm for splice junction detection using RNA-seq

Allows splice junction (SJ) detection. TrueSight is a method developed to improve sensitivity and specificity of mapping SJ spanning RNA-seq reads. The software incorporates information from (i) RNA-seq mapping quality and (ii) coding potentials from the reference genome sequences into a unified model that utilizes adaptive training by iterative logistic regression for de novo identification of SJs and filtering out unreliable SJs. It can accelerate the annotation of new genomes and helps to elucidate the origins of complex traits of different species.

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TrueSight forum

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TrueSight classification

TrueSight specifications

Unique identifier:
OMICS_01258
Interface:
Command line interface
Input format:
FASTQ
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Source code URL:
http://bioen-compbio.bioen.illinois.edu/TrueSight/truesight-v0.06.tar.gz
Software type:
Package/Module
Restrictions to use:
None
Output format:
BAM, SAM
License:
GNU General Public License version 3.0
Version:
0.06
Requirements:
Perl, GCC with Standard C++ Library, GNU make, samtools
Maintained:
Yes

TrueSight distribution

versioning

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No versioning.

TrueSight support

Maintainers

  • Ma Jian <>
  • Gene Robinson <>

Credits

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Publications

Institution(s)

Department of Bioengineering, University of Illinois at Urbana-Champaign, IL, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL, USA; Department of Entomology, University of Illinois at Urbana-Champaign, IL, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA; School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA; Department of Molecular and Biological Physics, Moscow Institute for Physics and Technology, Dolgoprudny, Moscow Region, Russia; Neuroscience Program, University of Illinois at Urbana-Champaign, IL, USA

Funding source(s)

Supported by National Science Foundation, National Institutes of Health [1R21HG006464, 1DP1OD006416 and 5R01HG00783].

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