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CIRCexplorer is a combined strategy to identify junction reads from back spliced exons and intron lariats.

Version: 1.1.10

Last Modified: 2016-7-14

Authors: Xiao-Ou Zhang (, Li Yang (

Maintainer: Xu-Kai Ma (

Download the latest stable version of CIRCexplorer

To see what has changed in recent versions of CIRCexplorer, see the CHANGELOG.


After one year’s tensive development, we have upgraded and extended CIRCexplorer to a new version – CIRCexplorer2, with many improvements and lots of new features. Welcome to use and cite it!

A schematic flow shows the pipeline



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. Other functions and supports for more aligners are under tensive developments. Thanks for your supports and understanding!


Software / Package

TopHat or STAR



The poly(A)−/ribo− RNA-seq is recommended. If you want to obtain more circular RNAs, RNase R treatment could be performed.


CIRCexplorer was originally developed as a circular RNA analysis toolkit supporting TopHat & TopHat-Fusion. After version 1.1.0, it also supports STAR.

TopHat & TopHat-Fusion

To obtain junction reads for circular RNAs, two-step mapping strategy was exploited:

tophat2 -a 6 --microexon-search -m 2 -p 10 -G knownGene.gtf -o tophat hg19_bowtie2_index RNA_seq.fastq
bamToFastq -i tophat/unmapped.bam -fq tophat/unmapped.fastq
tophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search hg19_bowtie1_index tophat/unmapped.fastq


To detect fusion junctions with STAR, --chimSegmentMin should be set to a positive value. For more details about STAR, please refer to STAR manual.


Option 1: using pip

pip install CIRCexplorer

Option 2: via conda

CIRCexplorer is available as conda package with:

conda install circexplorer --channel bioconda

Option 3: from docker container

Docker container:

docker run -it --rm

Option 4: in galaxy

If you have access to a Galaxy instance, CIRCexplorer is also available from the Galaxy Tool Shed.

Option 5: from source codes

1 Download CIRCexplorer

git clone
cd CIRCexplorer

2 Install required packages

pip install -r requirements.txt

3 Install CIRCexplorer

python install

Usage 1.1.10 -- circular RNA analysis toolkits.

Usage: [options]

    -h --help                      Show this screen.
    --version                      Show version.
    -f FUSION --fusion=FUSION      TopHat-Fusion fusion BAM file. (used in TopHat-Fusion mapping)
    -j JUNC --junc=JUNC            STAR Chimeric junction file. (used in STAR mapping)
    -g GENOME --genome=GENOME      Genome FASTA file.
    -r REF --ref=REF               Gene annotation.
    -o PREFIX --output=PREFIX      Output prefix [default: CIRCexplorer].
    --tmp                          Keep temporary files.
    --no-fix                       No-fix mode (useful for species with poor gene annotations)


TopHat & TopHat-Fusion -f tophat_fusion/accepted_hits.bam -g hg19.fa -r ref.txt

STAR Chimeric.out.junction fusion_junction.txt -j fusion_junction.txt -g hg19.fa -r ref.txt


Field Description
geneName Name of gene
isoformName Name of isoform
chrom Reference sequence
strand + or - for strand
txStart Transcription start position
txEnd Transcription end position
cdsStart Coding region start
cdsEnd Coding region end
exonCount Number of exons
exonStarts Exon start positions
exonEnds Exon end positions hg19/hg38/mm10 ref/kg/ens/fa out

Example (download hg19 RefSeq gene annotation file): hg19 ref ref.txt


See details in the example file

Field Description
chrom Chromosome
start Start of junction
end End of junction
name Circular RNA/Junction reads
score Flag to indicate realignment of fusion junctions
strand + or - for strand
thickStart No meaning
thickEnd No meaning
itemRgb 0,0,0
exonCount Number of exons
exonSizes Exon sizes
exonOffsets Exon offsets
readNumber Number of junction reads
circType ‘Yes’ for ciRNA, and ‘No’ for circRNA (before 1.1.0); ‘circRNA’ or ‘ciRNA’ (after 1.1.1)
geneName Name of gene
isoformName Name of isoform
exonIndex/intronIndex Index (start from 1) of exon (for circRNA) or intron (for ciRNA) in given isoform (newly added in 1.1.6)
flankIntron Left intron/Right intron

Note: The first 12 columns are in BED12 format.


Zhang XO, Wang HB, Zhang Y, Lu X, Chen LL and Yang L. Complementary sequence-mediated exon circularization. Cell, 2014, 159: 134-147


Copyright (C) 2014-2016 YangLab. See the LICENSE file for license rights and limitations (MIT).