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).
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.
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
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 |