Welcome to TRANSIT2’s documentation!

GitHub last tag

Transit2 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 TRANSIT2. Below are a few quick links to some of the most important sections of the documentation, followed by a brief overview of TRANSIT2’s features.

Note

TRANSIT2 is a re-implementation of the original version of TRANSIT, which is still being maintained for backwards-compatibility. TRANSIT2 has most of the same analytical methods, but it has an enhanced GUI. Also, some of the command-line arguments and flags have changed.

Features

TRANSIT2 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.

[** NEW **] CRISRPi ANALYSIS METHODS

PRE-PROCESSING

ANALYSES of single conditions

ANALYSES for pairwise comparisons

ANALYSES for multiple conditions

POST-PROCESSING

Support

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