CIRCexplorer2 annotate integrates CIRCexplorer into CIRCexplorer2. It annotates back-splicing junction reads with user provided gene annotations.

Usage and option summary


CIRCexplorer2 annotate [options] -r REF -g GENOME <circ_dir>


-h --help                      Show help message.
--version                      Show version.
-r REF --ref=REF               Gene annotation.
-g GENOME --genome=GENOME      Genome FASTA file.
--no-fix                       No-fix mode (useful for species with poor gene annotations).

Notes about options

  1. It would randomly report one circular RNA isoform for each back-splicing junction based on existed gene annotations.
  2. If you set --no-fix options, realignment step of fusion junction reads will be skipped. It is useful for species with poor gene annotations, but the accuracy of circular RNA prediction would decrease.


CIRCexplorer2 annotate will create one annotate folder under the <circ_dir> folder. The circ_fusion.txt contains the final circular RNA annotation information.

├── annotated_fusion.txt
└── circ_fusion.txt
  • annotated_fusion.txt: Annotated fusion junction information file.
  • circ_fusion.txt: Circular RNA annotation file.

Format of circ_fusion.txt:

Field Description
chrom Chromosome
start Start of circular RNA
end End of circular RNA
name Circular RNA/Junction reads
score Flag of fusion junction realignment
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 Type of circular RNA
geneName Name of gene
isoformName Name of isoform
index Index of exon or intron
flankIntron Left intron/Right intron