CIRCexplorer protocols

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 <>

Publication for CIRCexplorer

CIRCexplorer IN pipeline

2017
PMCID: 5520850
PMID: 28281539
DOI: 10.1038/cr.2017.31

[…] of the ip samples (m6a or eif4g2) was normalized by the mean coverage of entire gene, then divided by normalized coverage of corresponding window in control samples., we detected circrna using circexplorer pipeline. first reads were aligned to grch37 human genome with tophat, and then unmapped reads were realigned with tophat-fusion. finally, back-spliced junction reads were annotated […]

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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