CIRCexplorer specifications

Information


Unique identifier OMICS_10927
Name CIRCexplorer
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Poly(A)−/ribo− RNA-seq data
Input format FASTQ,BAM
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Version 1.1.3
Stability Stable
Requirements TopHat, TopHat-Fusion, STAR, bedtools, SAMtools, pysam, interval, docopt
Maintained Yes

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Maintainer


  • person_outline Li Yang <>

CIRCexplorer article

CIRCexplorer citation

2016
PMCID: 5153637

[…] with the ucsc genes annotation. unmapped reads were then extracted and mapped onto the relevant reference genome using tophat-fusion to detect the “fusion junctions”. the computational pipeline circexplorer was used to obtain back-spliced junction reads for circular rna prediction10. annovar was used to analyze the functional elements (exon, intron, 5′utr, etc.) from which the circrnas […]

CIRCexplorer institution(s)
Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Department of Orthopedic Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
CIRCexplorer funding source(s)
This work was supported by grants XDA01010206 and 2012OHTP08 from CAS; 2014CB964800, 2014CB910600, and 2011CBA01105 from MOST; 31322018 and 31271376 from NSFC; and 2012SSTP01 from SIBS.

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