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


No version available


  • person_outline Vinay Mittal
  • person_outline John McDonald

Publication for RNA-Seq analysis pipeline

R-SAP citations


De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion gene transcripts of potential functional significance

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

[…] ative analysis of fusion transcripts using RNA-Seq data, we designed a computational workflow (Fig. ) that integrates several existing bioinformatics tools including our previously published pipeline R-SAP []. The overall workflow is as follows:Fig. 1 […]


Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation

BMC Med Genomics
PMCID: 4504069
PMID: 26177635
DOI: 10.1186/s12920-015-0118-9

[…] , two breakpoints are detected each corresponding to the genomic locus participating in the SV formation. Validation and breakpoint detection were carried out using our previously developed pipeline, R-SAP (RNA-Seq analysis pipeline; []), that accurately detects fragmented alignments (split-mapping) representing potential gene fusions and/or genomic rearrangements. R-SAP modules were slightly modi […]

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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