denovo
CIRCexplorer2 denovo
parses circular RNA de novo assembly results to identify novel circRNAs and characterize various of alternative splicing events.
Usage and option summary
Usage:
CIRCexplorer2 denovo [options] -r REF -g GENOME -b JUNC [-d CUFF] [-o OUT]
Options:
-h --help Show help message.
--version Show version.
-r REF --ref=REF Gene annotation.
--as=AS Detect alternative splicing and output.
--as-type=AS_TYPE Only check certain type (CE/RI/ASS) of AS events.
--abs=ABS Detect alternative back-splicing and output.
-b JUNC --bed=JUNC Input file.
-d CUFF --cuff=CUFF assemble folder output by CIRCexplorer2 assemble. [default: '']
-m TOPHAT --tophat=TOPHAT TopHat mapping folder.
-n PLUS_OUT --pAplus=PLUS_OUT TopHat mapping directory for p(A)+ RNA-seq.
-o OUT --output=OUT Output Folder. [default: denovo]
-g GENOME --genome=GENOME Genome FASTA file.
--no-fix No-fix mode (useful for species with poor gene annotations).
--rpkm Calculate RPKM for cassette exons.
Notes about options
- If the
--cuff
is not set,CIRCexplorer2 denovo
will only use existing gene annotations to parse alternative splicing with setting--as
option. This way is not recommended, so please runCIRCexplorer2 assemble
beforeCIRCexplorer2 denovo
. - If you set
--abs
option,CIRCexplorer2 denovo
will characteriza the alternative back-splicing of circular RNAs. - If you set
--as
option, it will characterize the alternative splicing of circular RNAs, including 'cassette exons', 'retained introns', 'A5SS' and 'A3SS'. In this mode, you should also offer the path of TopHat mapping directory for p(A)-/p(A)+ RNA-seq via-m
/-n
option. By default, after setting--as
option, it will check all types of alternative splicing events. You could also indicate one type of alternative splicing events through the--as-type
option ('CE': 'cassette exons', 'RI': 'retained introns', 'ASS': 'A5SS' and 'A3SS'). - 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. - If
--rpkm
option is set, RPKM of cassette exons would be calculated.
Input
The input files are similar to those in CIRCexplorer2 annotate
command. See Annotate for more details.
Output
CIRCexplorer2 denovo
will create one denovo
folder under the <circ_dir>
folder.
denovo
├── combined_ref.txt
├── circularRNA_full.txt
├── annotated_circ.txt
└── novel_circ.txt
abs
├── a5bs.txt
└── a3bs.txt
as
├── all_exon_info.txt
├── all_intron_info.txt
├── all_A5SS_info.txt
└── all_A3SS_info.txt
combined_ref.txt
: combined gene annotation file (de novo assembled gene annotations and existing gene annotations).circularRNA_full.txt
: Circular RNA annotation file. (same as relevant file in Annotate))annotated_circ.txt
: CircRNAs with annotated back-splice sites.a5bs.txt
: Alternative 5' back-splice site information file.a3bs.txt
: Alternative 3' back-splice site information file.novel_circ.txt
: CircRNAs with one or two novel back-splice site(s).all_exon_info.txt
: Cassette exon information file.all_intron_info.txt
: Retained intron information file.all_A5SS_info.txt
: Alternative 5' splice site information file.all_A3SS_info.txt
: Alternative 3' splice site information file.
Format of annotated_circ.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 |
geneName | Name of gene |
Format of a5bs.txt
:
Field | Description |
---|---|
chrom | Chromosome |
start | Start of circular RNA |
end | End of circular RNA |
strand | Strand of circular RNA |
absSite | Alternative back-splice site |
absCount | back-spliced read counts |
PCU | Percent Circularized-site Usage |
Format of a3bs.txt
:
Field | Description |
---|---|
chrom | Chromosome |
start | Start of circular RNA |
end | End of circular RNA |
strand | Strand of circular RNA |
absSite | Alternative back-splice site |
absCount | back-spliced read counts |
PCU | Percent Circularized-site Usage |
Format of novel_circ.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 |
leftLabel | Label of circRNA start |
rightLabel | Label of circRNA end |
Format of all_exon_info.txt
:
Field | Description |
---|---|
chrom | Chromosome |
start | Start of cassette exon |
end | End of cassette exon |
name | Exon label |
score | No meaning |
strand | + or - for strand |
geneName | Name of gene |
isoformName | Name of isoform |
read | CircRNA fusion junction reads |
psiCirc | PSI in circular RNAs |
psiLinear | PSI in linear RNAs |
pValue1 | P value (circular RNAs vs linear RNAs) |
pValue2 | P value (linear RNAs vs circular RNAs) |
inCirc | Inclusion reads in circular RNAs |
exCirc | Exclusion reads in circular RNAs |
inLinear | Inclusion reads in linear RNAs |
exLinear | Exclusion reads in linear RNAs |
rpkmCirc | RPKM of cassette exon in circular RNAs |
rpkmLinear | RPKM of cassette exon in linear RNAs |
Format of all_intron_info.txt
:
Field | Description |
---|---|
chrom | Chromosome |
start | Start of retained intron |
end | End of retained intron |
name | Intron label |
score | No meaning |
strand | + or - for strand |
geneName | Name of gene |
isoformName | Name of isoform |
read | CircRNA fusion junction reads |
pirCirc | PIR in circular RNAs |
pirLinear | PIR in linear RNAs |
pValue1 | P value (circular RNAs vs linear RNAs) |
pValue2 | P value (linear RNAs vs circular RNAs) |
riCirc | Retained intron reads in circular RNAs |
juncCirc | Junction reads in circular RNAs |
intronCirc | Intron reads in circular RNAs |
riLinear | Retained intron reads in linear RNAs |
juncLinear | Junction reads in linear RNAs |
intronLinear | Intron reads in linear RNAs |
Format of all_A5SS_info.txt
:
Field | Description |
---|---|
chrom | Chromosome |
start | Start of circular RNA |
end | End of circular RNA |
strand | + or - for strand |
readCirc | 5' splice reads in circular RNAs |
totalCirc | Total splice reads in circular RNAs |
psuCirc | PSU in circular RNAs |
readLinear | 5' splice reads in linear RNAs |
totalLinear | Total splice reads in linear RNAs |
psuLinear | PSU in linear RNAs |
Format of all_A3SS_info.txt
:
Field | Description |
---|---|
chrom | Chromosome |
start | Start of circular RNA |
end | End of circular RNA |
strand | + or - for strand |
readCirc | 3' splice reads in circular RNAs |
totalCirc | Total splice reads in circular RNAs |
psuCirc | PSU in circular RNAs |
readLinear | 3' splice reads in linear RNAs |
totalLinear | Total splice reads in linear RNAs |
psuLinear | PSU in linear RNAs |