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R-SAP | A multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data

Studies and quantifies high-throughput RNA-Seq datasets. R-SAP employs a hierarchical decision-making procedure to characterize various classes of transcripts. It compares reference genome mappings of RNA-Seq reads with the genomic coordinates of known and well-annotated transcripts. It is able to recognize known and new RNA isoforms and, chimeric transcripts. This tool can discover alternative splicing (AS) and chimeric transcripts.

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R-SAP classification

R-SAP specifications

Unique identifier:
Software type:
Restrictions to use:
Input format:
Operating system:
Computer skills:
RNA-Seq analysis pipeline
Command line interface
Input data:
Some alignment files.
Output data:
Some transcript assignments for the sequencing reads, gene-expression levels, lists of aberrantly spliced genes and data statistics.
Programming languages:

R-SAP distribution


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R-SAP support


  • Vinay Mittal <>
  • John McDonald <>


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School of Biology, Georgia Institute of Technology, Atlanta, GA, USA; Parker H. Petit Institute for Bioengineering and Bioscience, Georgia institute of Technology, Atlanta, GA, USA; Ovarian Cancer Institute, Atlanta, GA, USA

Funding source(s)

Supported by Ovarian Cancer Institute; Ovarian Cycle, The Waterfall Foundation; Deborah Nash Harris Endowment Fund and Robinson Family Foundation.

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