Usage¶

Command overview¶

circfull <command> [options]

Supported commands:

RG: Reference-guided detection
DNSC: De novo self-correction to consensus sequence
cRG: Reference-guided detection using DNSC-corrected reads
strand: Identify transcript strand of circFL-seq reads
sRG: Reference-guided detection with stranded reads
mRG: Merge circRNA results from RG and cRG/sRG
anno: Annotate full-length circRNAs
geneExp: Quantify gene expression to evaluate linear RNA residuals
var: Call variants in circRNAs

Common workflow¶

Inputs¶

rawFq=M1.example.fq
cleanFq=M1.clean.fq
gtfFile=gencode.v19.annotation.sort.gtf.gz
genome=hg19.fa
thread=80
outDir=circFL_example

1. Trim/split raw reads¶

porechop-runner.py -t $thread -i $rawFq -o $cleanFq --barcode_threshold 95 --check_reads 1000

2. Detect full-length circRNA from clean reads (RG)¶

circfull RG -f $cleanFq -g $genome -a $gtfFile -t $thread -o $outDir

3. Identify strand information¶

circfull strand -f $rawFq -F $cleanFq -a $gtfFile -l 100 -t $thread -r $outDir -o $outDir

4. Detect from stranded reads (sRG)¶

circfull sRG -g $genome -a $gtfFile -s $outDir -t $thread -o $outDir

5. Build consensus with DNSC¶

circfull DNSC -f $cleanFq -t $thread -o $outDir
circfull DNSC -f $cleanFq -t $thread -o $outDir -c

6. Detect from DNSC consensus (cRG)¶

circfull cRG -f $outDir -g $genome -a $gtfFile -t $thread -o $outDir

7. Merge and filter circRNAs (mRG)¶

rmsk=rmsk.bed.gz
circfull mRG -f $cleanFq -g $genome -r $outDir -c $outDir -s $outDir -t $thread -o $outDir

8. Annotate full-length circRNAs¶

circfull anno -b ${outDir}/mRG/circFL_Normal_pass.bed -a $gtfFile -o ${outDir}/mRG/circFL_Normal_pass_anno.txt

9. Quantify gene expression¶

umgtfFile=gencode.v19.annotation.gtf
gene_ref=ref_gene.fa
createGeneRef $umgtfFile $genome $gene_ref
circfull geneExp -f $cleanFq -r $gene_ref -o $outDir -t $thread

10. Call variants¶

circfull var -f $cleanFq -g $genome -r $outDir -t $thread -o $outDir

Key command options¶

RG¶

circfull RG -f fastq -g genome -a anno [-u] [-t threads] [-r] [-o output]

DNSC¶

circfull DNSC -f fastq [-t threads] [-c] [-m mem] [-o output]

cRG¶

circfull cRG -f DNSC -g genome -a anno [-t threads] [-u] [-o output]

strand¶

circfull strand -f fastq -F fastq2 -a anno [-r RG_dir] [-l hang_len] [-t threads] [-o output]

sRG¶

circfull sRG -g genome -a anno [-s strandDir] [-t threads] [-r] [-o output]

mRG¶

circfull mRG -f fastq -g genome [-r RG] [-c cRG] [-s sRG] [-t threads] [-o output]

anno¶

circfull anno -b bed -a anno [-o output]

geneExp¶

circfull geneExp -f fastq -r ref [-t threads] [-o output]

var¶

circfull var -f fastq -g genome [-r RG_dir] [-t threads] [-o output]

Note: Higher thread counts increase memory usage.