Tobias

Introduction

Tobias is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data.

For more information, please check its website: https://biocontainers.pro/tools/tobias and its home page on Github.

Versions

• 0.13.3

Commands

• TOBIAS

Module

You can load the modules by:

module load biocontainers
module load tobias

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 Tobias on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=tobias
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers tobias

TOBIAS DownloadData --bucket data-tobias-2020
mv data-tobias-2020/ test_data/

TOBIAS PlotAggregate --TFBS test_data/BATF_all.bed \
     --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw \
     --output BATFJUN_footprint_comparison_all.pdf \
     --share_y both --plot_boundaries --signal-on-x

TOBIAS BINDetect --motifs test_data/motifs.jaspar \
     --signals test_data/Bcell_footprints.bw test_data/Tcell_footprints.bw \
     --genome test_data/genome.fa.gz \
     --peaks test_data/merged_peaks_annotated.bed \
     --peak_header test_data/merged_peaks_annotated_header.txt \
     --outdir BINDetect_output --cond_names Bcell Tcell --cores 8

TOBIAS ATACorrect --bam test_data/Bcell.bam \
    --genome test_data/genome.fa.gz \
    --peaks test_data/merged_peaks.bed \
    --blacklist test_data/blacklist.bed \
    --outdir ATACorrect_test --cores 8

TOBIAS FootprintScores --signal test_data/Bcell_corrected.bw \
    --regions test_data/merged_peaks.bed \
    --output Bcell_footprints.bw --cores 8