CIRIquant
Introduction
CIRIquant
is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data.
For more information, please check its | Docker hub: https://hub.docker.com/r/mortreux/ciriquant and its home page on Github.
Versions
1.1.2
Commands
CIRIquant
Module
You can load the modules by:
module load biocontainers
module load ciriquant
config.yml
All required dependencies have been installed within the CIRIquant container image. But users still need toprovide the PATH of these exectuables 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
Example job
Warning
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