Welcome to TRANSIT’s documentation!

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Transit is python-based software for analyzing TnSeq data (sequencing data from transposon mutant libraries) to determine essentiality of bacterial genes under different conditions.

This page contains the documentation for TRANSIT. Below are a few quick links to some of the most important sections of the documentation, followed by a brief overview of TRANSIT’s features.

Note

This documentation is for the original version of Transit. We recently released a new version of Transit called TRANSIT2 (re-implementation from scratch), which has most of the same TnSeq analytical methods, but it has an enhanced GUI. Nonetheless, this original version of TRANSIT is still being maintained for backwards-compatibility.

Features

TRANSIT offers a variety of features including:

  • More than 8 analysis methods, including methods for determining conditional essentiality as well as genetic interactions.
  • Ability to analyze himar1 or tn5 transposons datasets.
  • TrackView to help visualize read-counts accross the genome.
  • Can export datasets into a variety of formats, including IGV.
  • Includes a variety of normalization methods.
  • Quality Control diagnostics, to idenfity poor quality datasets.
  • Ability to install as a python package, to import and use in your own personal scripts.

ANALYSIS METHODS

Support

For any questions or comments, please contact Dr. Thomas Ioerger, ioerger@cs.tamu.edu.