Skip to main content

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

Project description

TOBIAS - Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

PyPI Version install with bioconda


ATAC-seq (Assay for Transposase-Accessible Chromatin using high-throughput sequencing) is a sequencing assay for investigating genome-wide chromatin accessibility. The assay applies a Tn5 Transposase to insert sequencing adapters into accessible chromatin, enabling mapping of regulatory regions across the genome. Additionally, the local distribution of Tn5 insertions contains information about transcription factor binding due to the visible depletion of insertions around sites bound by protein - known as footprints.

TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data, and includes:

  • Correction of Tn5 insertion bias
  • Calculation of footprint scores within regulatory regions
  • Estimation of bound/unbound transcription factor binding sites
  • Visualization of footprints within and across different conditions

For information on each tool, please see the wiki.


TOBIAS is written as a python package and can be quickly installed via pip:

pip install tobias

or directly from github using:

$ git clone
$ python install

Please see the installation page for more info.


All tools are available through the command-line as TOBIAS <TOOLNAME>, for example:


                                   TOBIAS ~ ATACorrect

ATACorrect corrects the cutsite-signal from ATAC-seq with regard to the underlying
sequence preference of Tn5 transposase.

TOBIAS ATACorrect --bam <reads.bam> --genome <genome.fa> --peaks <peaks.bed>

Output files:
- <outdir>/<prefix>
- <outdir>/<prefix>
- <outdir>/<prefix>
- <outdir>/<prefix>
- <outdir>/<prefix>_atacorrect.pdf


Command-line examples

These examples use the test data provided in the TOBIAS/test_data directory, so please make sure you are in the upper TOBIAS/ directory when running the commands.

ATACorrect: Bias correction of ATAC-seq reads in open chromatin

$ TOBIAS ATACorrect --bam test_data/Bcell_chr4.bam --genome test_data/genome_chr4.fa.gz --peaks test_data/merged_peaks.bed --blacklist test_data/blacklist_chr4.bed --outdir atacorrect_test --prefix Bcell --cores 8

FootprintScores: Calculate footprint scores from corrected cutsites

$ TOBIAS FootprintScores --signal test_data/ --regions test_data/merged_peaks.bed --output --cores 8

BINDetect: Estimation of differentially bound motifs based on scores, sequence and motifs

$ TOBIAS BINDetect --motifs test_data/example_motifs.txt --signals test_data/ test_data/ --genome test_data/genome_chr4.fa.gz --peaks test_data/annotated_peaks.bed --peak_header test_data/annotated_peaks_header.txt --outdir bindetect_output --cond_names Bcell Tcell --cores 8

PlotAggregate: Plot aggregated ATAC-seq signals in combinations of .bed/.bw to visualize footprints

Visualize the difference in footprints between two conditions for all accessible sites:

$ TOBIAS PlotAggregate --TFBS test_data/BATFJUN_all.bed  --signals test_data/ test_data/ --output BATFJUN_footprint_comparison_all.pdf --share_y both --plot_boundaries

Visualize the difference in footprints between two conditions exclusively for bound sites:

$ TOBIAS PlotAggregate --TFBS test_data/BATFJUN_Bcell_bound.bed test_data/BATFJUN_Tcell_bound.bed --signals test_data/ test_data/ --output BATFJUN_footprint_comparison_subsets.pdf --share_y both --plot_boundaries

Visualize the split of bound/unbound sites for one condition:

$ TOBIAS PlotAggregate --TFBS test_data/IRF1_all.bed test_data/IRF1_bound.bed test_data/IRF1_unbound.bed --signals test_data/ test_data/ test_data/ --output IRF1_footprint.pdf  --share_y sites --plot_boundaries

PlotHeatmap: Plot heatmaps and aggregates of ATAC-seq signals in combinations of .bed/.bw to visualize footprints

$ TOBIAS PlotHeatmap --TFBS test_data/BATFJUN_Bcell_bound.bed test_data/BATFJUN_Bcell_unbound.bed --TFBS test_data/BATFJUN_Tcell_bound.bed test_data/BATFJUN_Tcell_unbound.bed --signals test_data/ test_data/ --output BATFJUN_heatmap.pdf --signal_labels Bcell Tcell --share_colorbar

PlotTracks: Plot IGV-style genomic signals such as cutsites and footprints across a selection of regions

$ TOBIAS PlotTracks --bigwigs test_data/* --bigwigs test_data/* --regions test_data/plot_regions.bed --sites test_data/binding_sites.bed --highlight test_data/binding_sites.bed --gtf test_data/transcripts_chr4.gtf --colors red darkblue red darkblue

FormatMotifs: A utility to convert and join/split across different motif-file formats
Join individual motif files to one:

$ TOBIAS FormatMotifs --input test_data/individual_motifs/* --format pfm --task join --output example_motifs.txt

Split a motif file containing several motifs:

$ TOBIAS FormatMotifs --input test_data/example_motifs.txt --format pfm --task split --output split_motifs

Filter a larger motif file using TF names:

$ echo 'MAFK CTCF JUNB' > TF_names.txt
$ TOBIAS FormatMotifs --input test_data/example_motifs.txt --output filtered_motifs.txt --filter TF_names.txt

Cluster Motifs: Cluster motifs and create consensus motifs based on similarity

$ TOBIAS ClusterMotifs --motifs test_data/example_motifs.txt

Filter fragments from a .bam-file using a .bed-file of regions:

$ TOBIAS FilterFragments --bam test_data/Bcell_chr4.bam --regions test_data/peaks.bed

Snakemake pipeline

You can run each TOBIAS tool independently or as part of a pipeline. We provide a pre-set snakemake workflow which is found here.

Nextflow pipeline

You can also run the TOBIAS tool as a nextflow pipeline. The pre-set workflow can be found here.

kubernetes/de.NBI cloud aware pipeline

We also provide the TOBIAS nextflow pipeline for a cloud computing environment. There is one version utilising a kubernetes framework, and a second version utilizing a webbased job scheduler, started automatically within a local TOBIAS run, making use of the de.NBI cloud.


This project is licensed under the MIT license.


Mette Bentsen (mette.bentsen (at)

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for tobias, version 0.10.1
Filename, size File type Python version Upload date Hashes
Filename, size tobias-0.10.1.tar.gz (327.0 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page