R-SAP statistics

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R-SAP specifications

Information


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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Maintainers


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

Publication for RNA-Seq analysis pipeline

R-SAP in pipeline

2017
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. ) that integrates several existing bioinformatics tools including our previously published pipeline r-sap []. 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 […]


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R-SAP in publications

 (3)
PMCID: 5575902
PMID: 28851357
DOI: 10.1186/s12920-017-0289-7

[…] for high-quality rna-sequencing reads. reads were de novo assembled into contigs followed by reference genome mapping. chimeric transcripts were detected, filtered and characterized using our r-sap algorithm. the relative abundance of reads was used to estimate levels of gene expression., de novo assembly allowed for the accurate detection of 1959 chimeric transcripts to nucleotide level […]

PMCID: 4693159
PMID: 26473934
DOI: 10.3390/pathogens4040697

[…] acting in mucosal infections [,]., overall, the results of our studies evidenced that intravaginal immunization with recombinant mp65 mannoprotein (r mp65 r or secretory aspartyl proteinase (r sap2) conferred protection against vaginal candidiasis. below, we reported examples of experiments, already performed, of the kinetics of vaginal infection in rats immunized intravaginally […]

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 […]


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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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