Purdue University

Commands

• sicer
• sicer_df
• recognicer
• recognicer_df

Module

You can load the modules by:

module load biocontainers
module load sicer2

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 Sicer2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sicer2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers sicer2

sicer_df -t ./test/treatment_1.bed ./test/treatment_2.bed \ 
    -c ./test/control_1.bed ./test/control_2.bed \
    -s hg38 --significant_reads

recognicer_df -t ./test/treatment_1.bed ./test/treatment_2.bed \
    -c ./test/control_1.bed ./test/control_2.bed \
    -s hg38 --significant_reads