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 <circ_dir>
Options:
-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).
--low-confidence Extract low confidence circRNAs.
Notes about options
- It would randomly report one circular RNA isoform for each back-splicing junction based on existed gene annotations.
- 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
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 inlow_circ_fusion.txt
.
Input
CIRCexplorer2 annotate
needs a gene annotation file, a reference genome sequence file and a <circ_dir>
folder which contains fusion_junction.bed
created by CIRCexplorer2 parse
or CIRCexplorer2 align
.
<circ_dir>
└── fusion_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 one annotate
folder under the <circ_dir>
folder. The circ_fusion.txt
contains the final circular RNA annotation information.
annotate
├── annotated_fusion.txt
├── circ_fusion.txt
└── low_circ_fusion.txt (if set the '--low-confidence' option)
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 |
Format of low_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 |
leftInfo | Gene:Isoform:Index of left exon |
rightInfo | Gene:Isoform:Index of right exon |