sicer2
Link to section 'Introduction' of 'sicer2' Introduction
Sicer2 is the redesigned and improved ChIP-seq broad peak calling tool SICER.
For more information, please check its website: https://biocontainers.pro/tools/sicer2 and its home page on Github.
Link to section 'Versions' of 'sicer2' Versions
- 1.0.3
- 1.2.0
Link to section 'Commands' of 'sicer2' Commands
- sicer
- sicer_df
- recognicer
- recognicer_df
Link to section 'Module' of 'sicer2' Module
You can load the modules by:
module load biocontainers
module load sicer2
Link to section 'Example job' of '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