circRNA identification

Usage: ucircfull circ_call [--help] [--version] --mode STR [--notstranded VAR] --input FQ [--bam BAM] --ref REF --anno GTF [--umi CLSTR] --splice MOTIF --outdir DIR --prefix PREFIX --thread INT [--threshold INT] [--minimap2 PATH] [--samtools PATH] [--debug]

circRNA identification.

Optional arguments:
  -h, --help            shows help message and exits
  -v, --version         prints version information and exits
  -m, --mode STR        circRNA calling mode. (RG, ucRG, cRG) [required]
  -sn, --notstranded    find splicing signal in both strand. [default: false]
  -i, --input FQ        stranded fastq file. [required]
  --bam BAM             mapped bam file as input.
  -r, --ref REF         CIRI-long reference directory. [required]
  -a, --anno GTF        reference annotation GTF file. [required]
  -u, --umi CLSTR       umi clust results file. [default: "-"]
  --splice MOTIF        splice motifs. [default: "AGGT,AGGC,ACAT,ACGT,AGAT"]
  -o, --outdir DIR      output directory. [default: "."]
  -p, --prefix PREFIX   output prefix. [default: "circFL"]
  -t, --thread INT      number of threads used. [default: 4]
  --threshold INT       minimum supporting reads for a circRNA transcript. [default: 2]
  --minimap2 PATH       path to minimap2. [default: "minimap2"]
  --samtools PATH       path to samtools. [default: "samtools"]
  --debug               enable debug output.

ucircfull circ_call -m ucRG -i ${sample}_strand.fastq -r $genome -a $gtfFile -u ${sample}_umi.clstr -o ./ucRG -p $sample -t $thread

Output

• $sample.circ.gtf: identification and quantification results of circRNAs

• $sample.fusion.txt: detected fusion circRNAs

Output files

$prefix.circ.gtf

$prefix.circ.gtf is a standard GTF file generated by ucircfull circ_call. It contains three feature types for each reported circRNA locus:

• BSJ: back-splice junction locus, grouping all isoforms from the same BSJ site

• transcript: one full-length circRNA isoform (exon composition + splice-site variants)

• exon: exon structure of the isoform

The file uses the standard 9-column GTF layout:

Column	Description
1 seqname	Chromosome name
2 source	Always circfull
3 feature	BSJ, transcript, or exon
4 start	1-based start coordinate
5 end	1-based end coordinate
6 score	Always .
7 strand	Strand of the circRNA isoform
8 frame	Always .
9 attribute	Feature-specific attributes described below

Attributes written by ucircfull:

• BSJ records: gene_id, circ_type, host_gene_id, host_gene_name, bsj

• transcript records: gene_id, transcript_id, uniform_id, circ_type, host_gene_id, host_gene_name, bsj (per-isoform read count)

• exon records: gene_id, transcript_id, uniform_id, exon_number

Field meanings:

• gene_id: BSJ position ID in the format chr:start-end

• transcript_id: isoform ID in the format chr:start-end:strand|exon1_start-exon1_end,exon2_start-exon2_end,...

• bsj on BSJ records: total number of supporting reads summed across all isoforms at the BSJ locus

• bsj on transcript records: number of supporting reads for that isoform

• circ_type: circRNA classification (exon, intron, or intergenic_region)

• host_gene_id: best-matching host gene identifier from the annotation

• host_gene_name: gene symbol of the host gene

• uniform_id: standardized circRNA name following the proposed naming scheme; includes exon composition, splice-site variants (L/S), retained introns (RI), novel exons (NE), and an ordered .N suffix per distinct BSJ site (e.g. circAKT3(2,3).1, circMCU(2,L3).2)

• exon_number: exon order within the isoform, starting from 1

Only circRNA isoforms with supporting reads at or above the --threshold value are output to this file.

$prefix.fusion.txt

$prefix.fusion.txt is a tab-separated table describing fusion circRNAs detected by ucircfull circ_call.

Column	Description
circID	Fusion circRNA locus ID in the format chr_first|start_first|end_first|chr_second|start_second|end_second
isoID	Fusion isoform ID, including exon composition and strand for both loci
chr_first	Chromosome of the first fusion locus
start_first	Start coordinate of the first fusion locus
end_first	End coordinate of the first fusion locus
len_first	Length of the first fusion locus
exonNum_first	Number of exons in the first fusion locus
exon_start_first	Comma-separated exon start coordinates for the first locus
exon_end_first	Comma-separated exon end coordinates for the first locus
exon_leftSeq_first	Left splice-site sequence for each exon in the first locus
exon_rightSeq_first	Right splice-site sequence for each exon in the first locus
strand_first	Strand of the first fusion locus
geneName_first	Gene annotation overlapping the first locus, if available
chr_second	Chromosome of the second fusion locus
start_second	Start coordinate of the second fusion locus
end_second	End coordinate of the second fusion locus
len_second	Length of the second fusion locus
exonNum_second	Number of exons in the second fusion locus
exon_start_second	Comma-separated exon start coordinates for the second locus
exon_end_second	Comma-separated exon end coordinates for the second locus
exon_leftSeq_second	Left splice-site sequence for each exon in the second locus
exon_rightSeq_second	Right splice-site sequence for each exon in the second locus
strand_second	Strand of the second fusion locus
geneName_second	Gene annotation overlapping the second locus, if available
readCount	Number of reads supporting the fusion isoform
readID	Comma-separated read IDs supporting the fusion isoform