ciriquant
Link to section 'Introduction' of 'ciriquant' Introduction
CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data.
Docker hub: https://hub.docker.com/r/mortreux/ciriquant and its home page on Github.
Link to section 'Versions' of 'ciriquant' Versions
- 1.1.2
Link to section 'Commands' of 'ciriquant' Commands
- CIRIquant
Link to section 'Module' of 'ciriquant' Module
You can load the modules by:
module load biocontainers
module load ciriquant
Link to section 'config.yml ' of 'ciriquant' config.yml
All required dependencies have been installed within the CIRIquant container image. But users still need toprovide the PATH of these executables in `config.yml`. Please use the below `config.yml` as example:
name: hg38
tools:
bwa: /bin/bwa
hisat2: /bin/hisat2
stringtie: /bin/stringtie
samtools: /usr/local/bin/samtools
reference:
fasta: reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa
gtf: reference/Homo_sapiens.GRCh38.105.gtf
bwa_index: reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa
hisat_index: reference/hg38_hisat2
Link to section 'Example job' of 'ciriquant' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run CIRIquant on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 64
#SBATCH --job-name=ciriquant
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers ciriquant
CIRIquant -t 64 -1 SRR12095148_1.fastq -2 SRR12095148_2.fastq --config config.yml -o Output -p test