CIRCexplorer protocols

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CIRCexplorer specifications


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
TopHat, TopHat-Fusion, STAR, bedtools, SAMtools, pysam, interval, docopt
Maintained Yes



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  • person_outline Li Yang <>

Publication for CIRCexplorer

CIRCexplorer in pipeline

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 […]

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CIRCexplorer in publications

PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] from astrocytes microdissected from the posterior cingulate (pc) of alzheimer’s disease (ad) patients (n = 10) and healthy elderly controls (n = 10) using four circrna prediction algorithms - ciri, circexplorer, find_circ and knife., overall, utilizing these four tools, we identified a union of 4438 unique circrnas across all samples, of which 70.3% were derived from exonic regions. notably, […]

PMCID: 5888531
DOI: 10.1093/schbul/sby018.975

[…] circrna transcripts. sequencing libraries were constructed using illumina truseq rna library prep kit (lt) (150 cycles) and sequenced by an illumina nexseq500. sequencing data was analysed by the circexplorer2 pipeline to identify circrna transcripts. to validate the sequencing findings, real-time pcr was performed using outward primers sets designed to specifically amplify circular […]

PMCID: 5845222
PMID: 29523209
DOI: 10.1186/s13287-018-0793-5

[…] further differentiated to hipsc-cms by modulating wnt signaling in rpmi+b27 medium. following high-throughput rna sequencing, circrnas were extracted and quantified by a combined strategy known as circexplorer. integrative analysis was performed to illuminate the correlation between circrnas and their parental linear isoforms. cardiac and disease-specific expression of circrnas was confirmed […]

PMCID: 5844931
PMID: 29556495
DOI: 10.3389/fcell.2018.00020

[…] comparison of circrna pipelines was published (zeng et al., ), and we previously analyzed and compared the output from 5 different algorithms (hansen et al., ): circrna_finder (westholm et al., ), circexplorer (zhang et al., ), ciri (gao et al., ), find_circ (memczak et al., ), and mapsplice (wang et al., ). here, this analysis is extended by 6 additional algorithms: acsf (you et al., ), […]

PMCID: 5845524
PMID: 29682564
DOI: 10.1155/2018/8518563

[…] analyzed with nanodrop (thermo company, usa). circrna and small rna sequencing libraries were constructed with hiseq 2000 sequencing platform following the manufacturer's instructions., circexplorer software (version 1.1.7) [] was used to identify circrnas based on the fusion gene. after trimming adaptors, the small sequence fragments were mapped onto the human genome using bowtie […]

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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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