R-SAP pipeline

R-SAP specifications


Unique identifier OMICS_01409
Name R-SAP
Alternative name RNA-Seq analysis pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Some alignment files.
Input format PSL
Output data Some transcript assignments for the sequencing reads, gene-expression levels, lists of aberrantly spliced genes and data statistics.
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes


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  • person_outline Vinay Mittal <>
  • person_outline John McDonald <>

Publication for RNA-Seq analysis pipeline

R-SAP IN pipeline

PMCID: 5575902
PMID: 28851357
DOI: 10.1186/s12920-017-0289-7

[…] analysis of fusion transcripts using rna-seq data, we designed a computational workflow (fig. 1) that integrates several existing bioinformatics tools including our previously published pipeline r-sap [25]. the overall workflow is as follows:fig. 1 , rna-seq data may contain low-quality bases due to sequencing errors and fragments of sequencing adapters derived from failed or short cdna […]

R-SAP institution(s)
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
R-SAP 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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