https://github.com/gyjames/CIRI3
CIRI3 is a comprehensive analysis package for the detection and quantification of circRNAs in RNA-Seq data
--Reference
FASTA file of all reference sequences. Please make sure this file is the same one provided to BWA-MEM (required).
--Strigency
high strigency: only output circRNAs supported by more than 2 distinct PCC signals (default)
low strigency: only output circRNAs supported by more than 2 junction reads
no strigency: output all circRNAs regardless junction read or PCC signal counts
--Mapping quality
set threshold for mappqing quality of each segment of junction reads(default: 10; should be within [0,30])
--ChrM ID
tell CIRI3 the ID of mitochondrion in reference file(s) (default:chrM)
--Intronic circRNA
No: Skip the recognition of intronic self-ligated circRNA (default)
Yes: Perform the recognition of intronic self-ligated circRNA
result.txt is an information file for predicted circRNA.
Column 1: ID of a predicted circRNA in the pattern of "chr:start|end";
Column 2: chromosome of a predicted circRNA
Column 3: start loci of a predicted circRNA on the chromosome
Column 4: end loci of a predicted circRNA on the chromosome
Column 5: circular junction read (also called as back-spliced junction read) count of a predicted circRNA
Column 6: unique CIGAR types of a predicted circRNA. For example, a circRNAs have three junction reads: read A (80M20S, 80S20M), read B (80M20S, 80S20M), read C (40M60S, 40S30M30S, 70S30M), then its has two SM types (80S20M, 70S30M), two MS types (80M20S, 70M30S) and one SMS type (40S30M30S). Thus its SM_MS_SMS should be 2_2_1.
Column 7: non-junction read count of a predicted circRNA that mapped across the circular junction but consistent with linear RNA instead of being back-spliced
Column 8: ratio of circular junction reads calculated by 2*#junction_reads/(2*#junction_reads+#non_junction_reads).
Column 9: type of a circRNA according to positions of its two ends on chromosome (exon, intron or intergenic_region; only available when annotation file is provided)
Column 10: ID of the gene(s) where an exonic or intronic circRNA locates
Column 11: strand info of a pred