Sicer

Introduction

Sicer is a clustering approach for identification of enriched domains from histone modification ChIP-Seq data.

For more information, please check its website: https://biocontainers.pro/tools/sicer and its home page: http://home.gwu.edu/~wpeng/Software.htm.

Versions

1.1

Commands

SICER-df-rb.sh
SICER-df.sh
SICER-rb.sh
SICER.sh

Module

You can load the modules by:

module load biocontainers
module load sicer

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 Sicer on our clusters:

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

module --force purge
ml biocontainers sicer

SICER.sh ./ test.bed control.bed . hg18 1 200 150 0.74 600 .01

SICER-rb.sh ./ test.bed . hg18 1 200 150 0.74 400 100