CircMiner: Accurate and Rapid Detection of Circular RNA through Splice-Aware Pseudo-Alignment Scheme

A sensitive and fast computational tool for detecting circular RNAs (circRNAs) from RNA-Seq data.

Table of contents

1. Installation
2. Commands Options
3. Test Run
4. Example Commands
5. Output Files
6. Output Format
7. Contact & Support

Installation

BIOCONDA

CircMiner can be installed using conda package manager via bioconda channel:

conda install -c bioconda circminer

Installation from Source

Prerequisite. You will need (i) GCC 4.9.4 or higher; and (ii) GNU sort to compile the source code.

To install, you need to first fetch the git repository or download the corresponding compressed files.

git clone --recursive https://github.com/vpc-ccg/circminer.git
cd circminer
make 

Now you are ready to go!

Commands Options

Synopsis

circminer --index -r FASTA_FILE [OPTIONS]
circminer -r FASTA_FILE -g GTF_FILE -1 FASTQ_FILE_R1 -2 FASTQ_FILE_R2 [OPTIONS]

OPTIONS

Run circminer -h to see available options.

Indexing options

-i, --index:            Indicates the indexing stage.
-m, --compact-index:    Use this option only while building the index to enable compact version of the index.
-k, --kmer:     Kmer size [14..22] (default = 20).

General options:

-r, --reference:    Reference file.
-g, --gtf:      Gene model file.
-s, --seq:      Single-end sequence file.
-1, --seq1:     1st paired-end sequence file.
-2, --seq2:     2nd paired-end sequence file.

Advanced options:

-l, --rlen:     Max read length (default = 300).
-e, --max-ed:       Max allowed edit distance on each mate (default = 4).
-c, --max-sc:       Max allowed soft clipping on each mate (default = 7).
-w, --band:     Band width for banded alignment (default = 3).
-S, --seed-lim:     Skip seeds that have more than INT occurrences (default = 500).
-T, --max-tlen:     Maximum template length of concordant mapping. Paired-end mode only (default = 500).
-I, --max-intron:   Maximum length of an intron (default = 2000000).
-C, --max-chain-list:   Maximum number of chained candidates to be processed (default = 30).
-o, --output:       Prefix of output files (default = output).
-t, --thread:       Number of threads (default = 1).
-A, --sam:      Enables SAM output for aligned reads. Cannot be set along with --pam.
-P, --pam:      Enables custom pam output for aligned reads. Cannot be set along with --sam.
-d, --verbosity:    Verbosity mode: 0 or 1. Higher values output more information (default = 0).
-a, --scan-lev:     Transcriptome/Genome scan level: 0 to 2. (default = 0)
            0: Report the first mapping.
            1: Continue processing the read unless it is perfectly mapped to cDNA.
            2: Report the best mapping.

Other options:

-h, --help: Shows help message.
-v, --version:  Current version.

Test Run

To make sure CircMiner is successfully installed and runable on your machine, you can download a small sample test here. Unzip the downloaded package and use the following commands to run CircMiner for building the index and calling circRNAs.

Example Commands

Indexing reference genome:

$ ./circminer --index -r ref.fa -k 20 --thread 4

Mapping to reference genome and circRNA calling:

$ ./circminer -r ref.fa -g ref.gtf -1 R1.fq -2 R2.fq -o output

After a successful run output.circ_report should contain the following two lines:

Annotate CircMiner's output file

To annotate output.circ_report with the corresponding gene, transcript, and exon numbers please run the following script:

$ python scripts/annotate_transcript.py output.circ_report ref.gtf output.circ_report.annotated

Converting GTF file

If you use UCSC GTF files please use the following script to convert them to Ensembl GTF style and use the converted GTF when running CircMiner.

$ python scripts/convertGTF.py INPUT_GTF OUTPUT_GTF

Output Files

When a successful run finishes, the structure of output directory (e.g. outdir) will be as follows:

outdir                                         # output directory
├── output.circ_report                         # detected circRNA report
├── output.candidates.pam                      # back-splice juntion read mappings
└── output.mapping.pam/output.mapping.sam      # pseudo-alignment mapping results (only available when corresponding argument is passed)

Output Format

The information regarding the detected circRNAs is reported in output.circ_report file. It includes the exact breakpoint location, number of supporting back-splice junctions and their read names.

The back-splice juntion read mappings are stored in output.candidates.pam. If --pam/--sam is specified in the input arguments, the mapping results will be available in output.mapping.pam/output.mapping.sam file.

Note: If the scan level parameter (-a, --scan-lev) is set to 2 while running the tool, the mapping with the smallest error and soft-clip values is reported.

PAM mapping format:

Contact & Support

For any bug report, feature request, or questions please fill out an issue through CircMiner's issue page.

Citation

If you use CircMiner please cite our paper:

Asghari H., Lin YY., Xu Y., Haghshenas E., Collins CC., Hach F. CircMiner: Accurate and Rapid Detection of Circular RNA through Splice-Aware Pseudo-Alignment Scheme. Bioinformatics (2020). btaa232

Simulation Data

The simulated RNA-Seq reads used in this project can be accessed here.

Copyright and License

This software is released under GNU General Public License (v3.0).