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direct comparison of circular and linear RNA expression
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A computational pipeline for Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq (CLEAR)



Installation requirements


git clone
python ./ install


Start from fastq file:

usage: clear_quant [-h] -1 M1 [-2 M2] -g GENOME -i HISAT -j BOWTIE1 -G GTF
              [-o OUTPUT] [-p THREAD]

optional arguments:
  -h, --help            Show this help message and exit.
  -1 M1                 Comma-separated list of read sequence files in FASTQ
                        format. When running with pair-end read, this should
                        contain #1 mates.
  -2 M2                 Comma-separated list of read sequence files in FASTQ
                        format. -2 is only used when running with pair-end
                        read. This should contain #2 mates.
  -g GENOME, --genome GENOME
                        Genome FASTA file.
  -i HISAT, --hisat HISAT
                        Index files for HISAT2.
  -j BOWTIE1, --bowtie1 BOWTIE1
                        Index files for TopHat-Fusion.
  -G GTF, --gtf GTF     Annotation GTF file.
  -o OUTPUT, --output OUTPUT
                        The output directory.
  -p THREAD, --thread THREAD
                        Running threads. [default: 5]

Start from CIRCexplorer2 output file:

usage: circ_quant [-h] -c CIRC -b BAM -r REF [--threshold THRESHOLD]
                     [--ratio RATIO] [-l] [-t] [-o OUTPUT]

optional arguments:
  -h, --help            Show this help message and exit.
  -c CIRC, --circ CIRC  Input circular RNA file from CIRCexplorer2.
  -b BAM, --bam BAM     Input mapped reads from HISAT2 in BAM format.
  -r REF, --ref REF     The refFlat format gene annotation file.
  --threshold THRESHOLD
                        Threshold of FPB for choose circRNAs to filter linear
                        SJ.[default: 1]
  --ratio RATIO         The ratio is used for adjust comparison between circ
                        and linear.[default: 1]
  -l, --length          Whether to consider all reads' length? [default: False]
  -t, --tmp             Keep tmp dir? [default: False]
  -o OUTPUT, --output OUTPUT
                        Output file. [default: circRNA_quant.txt]


Start from fastq file:

clear_quant -1 mate_1.fastq -2 mate_2.fastq -g hg38.fa -i hg38.hisat_index -j hg38.bowtie_index -G annotation.gtf -o output_dir

Start from CIRCexplorer2 output file:

circ_quant -c CIRCexplorer2_output.txt -b hisat_aligned.bam -t -r annotation.refFlat -o quant.txt


  • output_dir/quant/quant.txt
Field Description
chrom Chromosome
start Start of circular RNA
end End of circular RNA
name Circular RNA/Junction reads
score Flag of fusion junction realignment
strand + or - for strand
thickStart No meaning
thickEnd No meaning
itemRgb 0,0,0
exonCount Number of exons
exonSizes Exon sizes
exonOffsets Exon offsets
readNumber Number of junction reads
circType Type of circular RNA
geneName Name of gene
isoformName Name of isoform
index Index of exon or intron
flankIntron Left intron/Right intron
FPBcirc Expression of circRNA
FPBlinear Expression of cognate linear RNA
CIRCscore Relative expression of circRNA


Ma XK*, Wang MR, Liu CX, Dong R, Carmichael GG, Chen LL and Yang L#. A CLEAR pipeline for direct comparison of circular and linear RNA expression. 2019, bioRxiv doi: 10.1101/668657


Copyright (C) 2019 YangLab. Licensed GPLv3 for open source use or contact YangLab ( for commercial use.

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