CIRCpseudo

CIRCpseudo is a pipeline to map back-splicing junction sequences for circRNA-derived pseudogenes detection. Using this pipeline, you could previously detect candidate circRNA-derived pseudogenes in genome, after maual check you could do further characterizations for them.

A schematic flow shows the pipeline

Features

Not specific to certain species
Aim to circRNA-derived pseudogenes detection

Usage: perl CIRCpseudo.pl [options]

Required:
        --circ          CircRNA file (CIRCexplorer format file)
        --ref           Reference annotation file (refFlat format file)
        --genome        Reference genome file (Fasta format file)
        --bwaidx        Bwa index of reference genome
        --output        Output file
Optional:
        --mismatch      max mismaches between fusion sequences and genome, defalt 4
        --fusionlen     fusion lenth of back-splice exon-exon junctions defalt 40

*Please add the CIRCpseudo directory to your $PATH first.

Example

CIRCpseudo.pl -circ circRNA.bed -ref mm10_ref.txt -genome mm10.fa -bwaidx index/mm10.fa.idx -output mouse_pseudo.txt

Note

ref.txt is in the format (Gene Predictions and RefSeq Genes with Gene Names) below (see details in the example file)

Field	Description
geneName	Name of gene
isoformName	Name of isoform
chrom	Reference sequence
strand	+ or - for strand
txStart	Transcription start position
txEnd	Transcription end position
cdsStart	Coding region start
cdsEnd	Coding region end
exonCount	Number of exons
exonStarts	Exon start positions
exonEnds	Exon end positions

mm10.fa is genome sequence in FASTA format.

Results

You should get result file by --output. Output file will report Host gene location, Host gene name, Fusion sequence, Pseudogene location and Mismatches.

Requirements

CircRNA file in CIRCexplorer format
Perl v5.14.1
Bowtie v0.12.9
BWA v0.6.2
bedtools v2.19.0

Citation

Dong R, Zhang XO, Zhang Y, Ma XK, Chen LL and Yang L. CircRNA-derived pseudogenes. Cell Res, 2016

bioCKO/CIRCpseudo