Import from CIRIquant

DEBKS can import circular junction count (CJC) and linear junction count (LJC) matrices from CIRIquant results with the optional prep_DEBKS utilities provided in the DEBKS repository.

Required scripts

The repository includes:

  • script/prep_DEBKS

  • script/prep_DEBKS.py

These utilities are adapted for CIRIquant result preparation.

Placement

Place the helper files into the CIRIquant installation paths:

  • prep_DEBKS.py into the CIRIquant library directory

  • prep_DEBKS into the CIRIquant executable/bin directory

Usage

Prepare CIRIquant output files list

CONTROL1 ./c1/c1.gtf C 1
CONTROL2 ./c2/c2.gtf C 2
CONTROL3 ./c3/c3.gtf C 3
CASE1 ./t1/t1.gtf T 1
CASE2 ./t2/t2.gtf T 2
CASE3 ./t3/t3.gtf T 3

The first three columns is required by default. For paired sample, the fourth column is required to specify the pairing information. For unpaired sample, the fourth column can be omitted.

Run prep_DEBKS

prep_DEBKS -i FILE --lib FILE --circ FILE --bsj FILE --fsj FILE --ratio FILE

Options:

  • -i FILE: input sample list

  • --lib FILE: output library information file

  • --circ FILE: output circRNA annotation file, typically merge_pos.txt

  • --bsj FILE: output circRNA back-splice junction counts, typically merge_circ.txt

  • --fsj FILE: output forward-splice/linear junction counts, typically merge_linear.txt

  • --ratio FILE: output circRNA junction-ratio matrix

Outputs for downstream DEBKS analysis

Typical generated files are:

  • merge_pos.txt

  • merge_circ.txt

  • merge_linear.txt

These outputs can be used as follows:

  • Use merge_pos.txt with DEBKS anno to annotate circRNAs and infer lengths.

  • Use merge_circ.txt and merge_linear.txt with DEBKS dec to detect DE circRNAs.