CircPlex is a tool for reconstrcuting circular RNA sequence from Rolling Circle Amplification (RCA) long reads. The data and scripts for reproducing the results of the paper are available here.
CircPlex requires C++11, KMC (version 3.2.4), EquiRep (version 1.0.0) and minimap2 (version 2.24) or later to compile and run successfully. Make sure your compiler supports C++11 by checking its version.
Clone the git repository of CircPlex using the command:
git clone https://github.com/Shao-Group/CircPlex.git
CircPLex uses KMC, EquiRep and Minimap2 as dependencies.
To install KMC, visit (https://github.com/refresh-bio/KMC).
To install EquiRep (license), visit (https://github.com/Shao-Group/EquiRep).
To install minimap2 (license), visit (https://github.com/lh3/minimap2).
CircPlex processes an input FASTA/FASTQ file and generates an output FASTA file with the circular RNA seqeunces and a TSV file with the circular RNA BSJs.
The usage of CircPlex is:
./CircPlex.sh <input_fasta_file> <output_file_prefix> <kmc-path> <equirep-path> <minimap2-path>
Arguments:
<input_file> - Path to the input FASTA/FASTQ file.
<output_file_prefix> - Prefix for the output FASTA file and the output BSJ file.
<kmc-path> - Path to KMC excutables directory.
<equirep-path> - Path to EquiRep executable directory.
<minimap2-path> - Path to minimap2 executable directory.
A small example of input data input.fasta is available in the example directory.
Commands to enter example directory and run CircPlex using input.fasta as input:
cd CircPlex
./CircPlex.sh ./example/input.fasta ./example/output <kmc-path> <equirep-path> <minimap2-path>
Two output files named output_circRNA_seqs.fasta and output_circRNA_bsjs.tsv will appear in the example directory.