Ananse

Introduction

ANANSE is a computational approach to infer enhancer-based gene regulatory networks (GRNs) and to identify key transcription factors between two GRNs.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/ananse

Home page: https://github.com/vanheeringen-lab/ANANSE

Versions

• 0.4.0

Commands

• ananse

Module

You can load the modules by:

module load biocontainers
module load ananse

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 ananse on our clusters:

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

module --force purge
ml biocontainers ananse

mkdir -p ANANSE.REMAP.model.v1.0
wget https://zenodo.org/record/4768075/files/ANANSE.REMAP.model.v1.0.tgz
tar xvzf ANANSE.REMAP.model.v1.0.tgz -C ANANSE.REMAP.model.v1.0
rm ANANSE.REMAP.model.v1.0.tgz

wget https://zenodo.org/record/4769814/files/ANANSE_example_data.tgz
tar xvzf ANANSE_example_data.tgz
rm ANANSE_example_data.tgz

ananse binding -H ANANSE_example_data/H3K27ac/fibroblast*bam -A ANANSE_example_data/ATAC/fibroblast*bam -R ANANSE.REMAP.model.v1.0/ -o fibroblast.binding
ananse binding -H ANANSE_example_data/H3K27ac/heart*bam -A ANANSE_example_data/ATAC/heart*bam -R ANANSE.REMAP.model.v1.0/ -o heart.binding

ananse network -b  fibroblast.binding/binding.h5 -e ANANSE_example_data/RNAseq/fibroblast*TPM.txt -n 4 -o fibroblast.network.txt
ananse network -b  heart.binding/binding.h5 -e ANANSE_example_data/RNAseq/heart*TPM.txt -n 4 -o heart.network.txt

ananse influence -s fibroblast.network.txt -t heart.network.txt -d ANANSE_example_data/RNAseq/fibroblast2heart_degenes.csv -p -o fibroblast2heart.influence.txt