DeamTools

Getting started

  • Installation
    • Requirements
    • Install DeamTools
    • Python dependencies
    • Verify installation
    • Running tests

Commands

  • index
    • Synopsis
    • Arguments
    • Requirements
    • How it works
    • Outputs
    • Examples
    • Notes
  • align
    • Synopsis
    • Required inputs
    • Optional arguments
    • Requirements
    • How it works
    • Examples
    • Notes
  • bam2bw
    • Synopsis
    • Required inputs
    • Optional arguments
    • Input file preparation
    • Examples
    • Output
    • Choosing parameters
  • bam2fragment
    • Synopsis
    • Required inputs
    • Optional arguments
    • Output format
    • Examples
    • Notes
  • qc
    • Synopsis
    • Required inputs
    • Optional arguments
    • Output control
    • Input file preparation
    • Examples
    • Metrics
    • Output
    • Choosing parameters
    • Schema 2.0: definitions and missing values
    • Deaminase and alignment diagnostics
    • Compare multiple samples
    • Interpretation rules
    • Portable directory output
  • match
    • Synopsis
    • Required inputs
    • Optional arguments
    • Requirements
    • How it works
    • Output
    • Examples
    • Notes
  • footprint
    • Synopsis
    • Required inputs
    • Optional arguments
    • How it works
    • Output
    • Examples
    • Notes
  • seq2edit
    • Synopsis
    • Required inputs
    • Optional arguments
    • How it works
    • Outputs
    • Examples
    • Notes

Reference

  • Algorithm
    • Biological basis
    • Strand convention
    • Deamination-aware alignment (index + align)
    • Edit detection conventions
    • Tn5 cut sites (bam2bw --event tn5)
    • Signal generation (bam2bw)
    • Enzyme sequence bias
    • Parallelism and output
    • Complexity
  • API reference
    • deamtools.align.index
    • deamtools.align.align
    • deamtools.preprocessing.bam2bw
    • deamtools.preprocessing.bam2fragment
    • deamtools.qc
    • deamtools.motif.match
    • deamtools.footprint
    • deamtools.utils
DeamTools
  • Search

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