annotate

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

Usage and option summary

Usage:

CIRCexplorer2 annotate [options] -r REF -g GENOME -b JUNC [-o OUT]

Options:

-h --help                      Show help message.
--version                      Show version.
-r REF --ref=REF               Gene annotation.
-g GENOME --genome=GENOME      Genome FASTA file.
-b JUNC --bed=JUNC             Input file.
-o OUT --output=OUT            Output file. [default: circularRNA_known.txt]
--no-fix                       No-fix mode (useful for species with poor gene annotations).
--low-confidence               Extract low confidence circRNAs.

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.
  3. CIRCexplorer2 annotate extracts fusion junction reads exactly matching the boundaries of exons of the same isoform by default. If you set the --low-confidence, it will also extract fusion junction reads matching the boundaries of exons of the different isofoms of the same gene, and output them in low_conf_circularRNA_known.txt.

Input

CIRCexplorer2 annotate needs a gene annotation file, a reference genome sequence file and a back_spliced_junction.bed created by CIRCexplorer2 parse or CIRCexplorer2 align.

back_spliced_junction.bed

Format of gene annotation file:

The file is in the format of Gene Predictions and RefSeq Genes with Gene Names below.

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

Output

CIRCexplorer2 annotate will create a circularRNA_known.txt file by default. The circularRNA_known.txt contains the final circular RNA annotation information.

circularRNA_known.txt
low_conf_circularRNA_known.txt
  • circularRNA_known.txt: Circular RNA annotation file.

Format of circularRNA_known.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

Format of low_conf_circularRNA_known.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
leftInfo Gene:Isoform:Index of left exon
rightInfo Gene:Isoform:Index of right exon