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A combined strategy to identify junction reads from back spliced exons and intron lariats. CIRCexplorer is now only a circular RNA annotating tool, and it parses fusion junction information from mapping results of other aligners. The result of circular RNA annotating is directly dependent on the mapping strategy of aligners. Different aligners may have different circular RNA annotations. CIRCexplorer is now only in charge of giving fusion junctions a correct gene annotation.

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CIRCexplorer classification

CIRCexplorer specifications

Software type:
Restrictions to use:
Input format:
MIT License
TopHat, TopHat-Fusion, STAR, bedtools, SAMtools, pysam, interval, docopt
Command line interface
Input data:
Poly(A)−/ribo− RNA-seq data
Operating system:
Computer skills:

CIRCexplorer distribution


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CIRCexplorer support


  • Li Yang <>


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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

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.

Link to literature

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