Usage

Command overview

DEBKS (merge | count | anno | dec) [options]

Commands:

  • merge: merge circRNA junction information from other software outputs

  • count: count linear junctions from BAM files

  • anno: annotate circRNA positions and infer lengths

  • dec: detect differentially expressed circRNAs

merge

DEBKS merge (-s software | -d designate) (-n name | -f file) [-b pos_based] [-o output]

Example:

DEBKS merge -s CIRI2 -n s1.ciri,s2.ciri,s3.ciri

count

DEBKS count -c circ_pos (-n name | -f file) [-l library_type] [-t threads] [-a hangover_len] [-o output]

Example:

DEBKS count -c merge_pos.txt -n s1.sort.bam,s2.sort.bam,s3.sort.bam

anno

DEBKS anno -c circ_pos -g gene_anno -m genome [-o output]

Example:

DEBKS anno -c merge_pos.txt -m hg19.fa -g gencode.v19.annotation.sort.gtf.gz

dec

DEBKS dec -c circ (-l linear | --c2 circ2) [-p] [-n sample_num] [-f filter] [-t threads] [-d cutoff] [-r read_len] [-a hangover_len] [-e circ_len] [--e2 circ2_len] [-o output]

Example:

DEBKS dec -c merge_circ.txt -l merge_linear.txt -n 3,3 -f 12 -t 20 -e anno_len.txt

Notes:

  • --c2 and -l are mutually exclusive.

  • -e and --e2 provide circRNA lengths to adjust junction-ratio calculation.

DEC output fields

Field

Description

chr

chromosome of circRNA

start

coordinate of start back-spliced site

end

coordinate of end back-spliced site

cjc_1

circular-junction counts in group 1

cjc_2

circular-junction counts in group 2

ljc_1 or cjc2_1

linear or circular2 junction counts in group 1

ljc_2 or cjc2_2

linear or circular2 junction counts in group 2

adj_cjc_len

length-adjust term for cjc

adj_ljc_len

length-adjust term for ljc

pbsi1

circular-junction ratio in group 1

pbsi2

circular-junction ratio in group 2

delta_pbsi

average difference between pbsi1 and pbsi2

P

significance of delta_pbsi

FDR

Benjamini-Hochberg corrected FDR

For importing CIRIquant outputs into DEBKS, see Import from CIRIquant.