Output files

File name	Details
circFL_Normal.txt	Normal circRNA isoforms detected by RG, cRG, sRG
circFL_Normal_pass.txt	Final circRNA isoforms from mRG
circFL_Fusion.txt	Fusion circRNA isoforms detected by RG
novoCluster.txt	CircRNA isoforms detected by DNSC with -c
circ_Var.txt	Variants in circRNAs detected by var
geneCountDf.txt	Gene expression quantified by geneExp
strandedFq.fastq	Transcript-strand circFL-seq reads from strand
circ_anno.txt	Full-length circRNA annotations from anno

circFL_Normal.txt / circFL_Normal_pass.txt

No.	Column	Details
1	circID	circRNA ID
2	isoID	isoform ID
3	chr	Chromosome
4	start	Start coordinate
5	end	End coordinate
6	len	circRNA length
7	exonNum	Number of exons
8	exon_start	Exon start coordinates
9	exon_end	Exon end coordinates
10	motif	Back-splice motif
11	leftSeq	Start-junction motif
12	rightSeq	End-junction motif
13	exon_leftSeq	Exon-start-junction motif
14	exon_rightSeq	Exon-end-junction motif
15	strand	Strand
16	geneName	Gene name
17	readCount	Supporting read count
18	readID	Supporting read IDs

circFL_Fusion.txt

No.	Column	Details
1	circID	circRNA ID
2	isoID	Isoform ID
3	chr_first	Chromosome of first locus
4	start_first	Start coordinate of first locus
5	end_first	End coordinate of first locus
6	len_first	Length of first locus
7	exonNum_first	Exon number of first locus
8	exon_start_first	Exon start coordinates (first locus)
9	exon_end_first	Exon end coordinates (first locus)
10	exon_leftSeq_first	Exon start-junction motif (first locus)
11	exon_rightSeq_first	Exon end-junction motif (first locus)
12	strand_first	Strand of first locus
13	geneName_first	Gene name of first locus
14	chr_second	Chromosome of second locus
15	start_second	Start coordinate of second locus
16	end_second	End coordinate of second locus
17	len_second	Length of second locus
18	exonNum_second	Exon number of second locus
19	exon_start_second	Exon start coordinates (second locus)
20	exon_end_second	Exon end coordinates (second locus)
21	exon_leftSeq_second	Exon start-junction motif (second locus)
22	exon_rightSeq_second	Exon end-junction motif (second locus)
23	strand_second	Strand of second locus
24	geneName_second	Gene name of second locus
25	readCount	Supporting read count
26	readID	Supporting read IDs

novoCluster.txt

No.	Column	Details
1	ID	Read ID
2	cluster	Cluster ID
3	strand	1/0 for sense/antisense transcript strand
4	readLen	Read length
5	start	Start of tandem repeats
6	end	End of tandem repeats
7	consLen	Consensus length
8	copyNum	Tandem repeat copy number
9	usage	Proportion of tandem repeats
10	consensus	Consensus sequence

circ_Var.txt

No.	Column	Details
1	isoID	Isoform ID
2	chr	Chromosome
3	pos	Variant coordinate
4	ref	Reference base
5	alt	Alternative base
6	refCount	Reads supporting reference base
7	altCount	Reads supporting alternative base
8	ratio	Alternative-base ratio

geneCountDf.txt

No.	Column	Details
1	geneID	Ensembl gene ID
2	geneName	Gene name
3	num	Supporting read count
4	ratio	Read count ratio among genes

circ_anno.txt

No.	Column	Details
1	chr	Chromosome
2	start	Start coordinate
3	end	End coordinate
4	isoID	Isoform ID
5	strand	Strand
6	exon_start	Exon start coordinates
7	exon_end	Exon end coordinates
8	len	circRNA length
9	start_type	Start-site annotation type
10	end_type	End-site annotation type
11	geneName	Gene name
12	detail_type	Detailed isoform annotation