Tool overview

An overview of all TOBIAS subtools can be found by running TOBIAS without parameters (or using --help):

$ TOBIAS
 ______________________________________________________________________________
|                                                                              |
|                                ~ T O B I A S ~                               |
|                   Transcription factor Occupancy prediction                  |
|                       By Investigation of ATAC-seq Signal                    |
|______________________________________________________________________________|

Usage: TOBIAS <TOOLNAME> [arguments]

Tools for footprinting analysis:
   ATACorrect           Correct reads with regards to Tn5 sequence bias
   ScoreBigwig          Calculate scores such as footprints from cutsites
   BINDetect            Detect TF binding from footprints and motifs

Tools for working with motifs/TFBS:
   TFBScan              Identify positions of TFBS given sequence and motifs
   FormatMotifs         Utility to deal with motif files
   ClusterMotifs        Cluster motifs by similarity
   ScoreBed             Score .bed-file with signal from .bigwig-file(s)

Visualization tools:
   PlotAggregate        Aggregate of .bigwig-signal across TF binding sites
   PlotHeatmap          Heatmap of .bigwig-signal across TF binding sites
   PlotChanges          Plot changes in TF binding across multiple conditions (from BINDetect output)
   PlotTracks           Plot genomic tracks using the svist4get package

Miscellaneous tools:
   DownloadData         Download test data for the TOBIAS tools
   MergePDF             Merge pdf files to one
   MaxPos               Get .bed-positions of highest bigwig signal within .bed-regions
   SubsampleBam         Subsample a .bam-file using samtools
   CreateNetwork        Create TF-gene network from annotated TFBS
   Log2Table            Convert logs from PlotAggregate to tab-delimitered tables of footprint stats
   FilterFragments      Tool for filtering fragments from a .bam-file based on the overlap of reads with .bed-regions

For help on each tool, please run: TOBIAS <TOOLNAME> --help
For version number: TOBIAS --version