Package: tobias
TOBIAS - Transcription factor Occupancy prediction By Investigation of ATAC-seq SignalIntroductionATAC-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 asfootprints.TOBIASis a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data, and includes:Correction of Tn5 insertion biasCalculation of footprint scores within regulatory regionsEstimation of bound/unbound transcription factor binding sitesVisualization of footprints within and across different conditionsFor information on each tool, please see thewiki.InstallationTOBIAS is written as a python package and can be quickly installed via pip:$pipinstalltobiasTOBIAS is also available as a conda package on the Bioconda channel:$condainstalltobias-cbiocondaPlease see theinstallationpage for more info.UsageAll tools are available through the command-line asTOBIAS <TOOLNAME>, for example:$ TOBIAS ATACorrect
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                                   TOBIAS ~ ATACorrect
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ATACorrect corrects the cutsite-signal from ATAC-seq with regard to the underlying
sequence preference of Tn5 transposase.

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

Output files:
- <outdir>/<prefix>_uncorrected.bw
- <outdir>/<prefix>_bias.bw
- <outdir>/<prefix>_expected.bw
- <outdir>/<prefix>_corrected.bw
- <outdir>/<prefix>_atacorrect.pdf

(...)Overview and command-line examplesATACorrect: Bias correction of ATAC-seq reads in open chromatinScoreBigwig: Calculate footprint scores from corrected cutsitesBINDetect: Estimation of differentially bound motifs based on scores, sequence and motifsPlotAggregate: Plot aggregated ATAC-seq signals in combinations of .bed/.bw to visualize footprintsPlotHeatmap: Plot heatmaps and aggregates of ATAC-seq signals in combinations of .bed/.bw to visualize footprintsPlotTracks: Plot IGV-style genomic signals such as cutsites and footprints across a selection of regionsFormatMotifs: A utility to convert and join/split across different motif-file formatsClusterMotifs: Cluster motifs and create consensus motifs based on similarityCreateNetwork: Create TF-TF binding network from annotated TFBSFilterFragments: Filter fragments from a .bam-file using a .bed-file of regionsAdditional utility toolsPipelinesWhile each TOBIAS tool can be run independently, they are developed to be run as part of an analysis pipeline. We provide ready-made pipelines for performing bias-correction, footprinting, differential binding and visualization for multiple conditions automatically.Snakemake pipelineWe provide a pre-set snakemake workflow which is foundhere.Nextflow pipelineYou can also run the TOBIAS tool as a nextflow pipeline. The pre-set workflow can be foundhere.Nextflow kubernetes/de.NBI cloud aware pipelineWe also provide the TOBIAS nextflow pipeline for a cloud computing environment. One version utilizes akubernetes framework, and a second version utilizing a webbased job scheduler, started automatically within a local TOBIAS run, making use of the de.NBIcloud.HelpIn case of any issues/questions/comments, please check out theFAQ. Otherwise, please write an issuehere.How to citeBentsen, M., Goymann, P., Schultheis, H. et al. ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. Nat Commun 11, 4267 (2020).DOI:https://doi.org/10.1038/s41467-020-18035-1LicenseThis project is licensed under theMIT license.ContactMette Bentsen (mette.bentsen (at) mpi-bn.mpg.de)