


Running TRANSIT
===============


|

GUI Mode
--------
To run TRANSIT in GUI mode (should be the same on Linux, Windows and MacOS), from the command line run:

::

    
    python PATH/src/transit.py

where PATH is the path to the TRANSIT installation directory. You might be able to double-click on icon for transit.py, if your OS associates .py files with python and automatically runs them. Note, because TRANSIT has a graphical user interface, if you are trying to run TRANSIT across a network, for example, running on a unix server but displaying on a desktop machine, you will probably need to use 'ssh -Y' and a local X11 client (like Xming or Cygwin/X on PCs).


|

Command line Mode
-----------------
TRANSIT can also be run from the command line, without the GUI interface. This is convenient if you want to run many analyses in batch, as you can write a script that automatically runs that automatically runs TRANSIT from the command line. TRANSIT expects the user to specify which analysis method they wish to run. The user can choose from "gumbel", "hmm", or "resampling". By choosing a method, and adding the "-h" flag, you will get a list of all the necessary parameters and optional flags for the chosen method:

::

    python PATH/src/transit.py gumbel -h




|

Gumbel
~~~~~~

To run the Gumbel analysis from the command line, type "python PATH/src/transit.py gumbel" followed by the following arguments:


+----------------+----------------+----------------+----------------+----------------+
| Argument       | Type           | Description    | Default        | Example        |
+================+================+================+================+================+
| annotation     | Required       | Path to        |                | genomes/H37Rv. |
|                |                | annotation     |                | prot\_table    |
|                |                | file in        |                |                |
|                |                | .prot\_table   |                |                |
|                |                | format         |                |                |
+----------------+----------------+----------------+----------------+----------------+
| control\_files | Required       | Comma-separate |                | data/glycerol\ |
|                |                | d              |                | _reads\_rep1.w |
|                |                | list of paths  |                | ig,data/glycer |
|                |                | to the \*.wig  |                | ol\_reads\_rep |
|                |                | replicate      |                | 2.wig          |
|                |                | datasets       |                |                |
+----------------+----------------+----------------+----------------+----------------+
| output\_file   | Required       | Name of the    |                | results/gumbel |
|                |                | output file    |                | \_glycerol.dat |
|                |                | with the       |                |                |
|                |                | results.       |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -s SAMPLES     | Optional       | Number of      | 10000          | -s 20000       |
|                |                | samples to     |                |                |
|                |                | take.          |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -m MINREAD     | Optional       | Smallest       | 1              | -m 2           |
|                |                | read-count     |                |                |
|                |                | considered to  |                |                |
|                |                | be an          |                |                |
|                |                | insertion.     |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -b BURNIN      | Optional       | Burn in        | 500            | -b 100         |
|                |                | period, Skips  |                |                |
|                |                | this number of |                |                |
|                |                | samples before |                |                |
|                |                | getting        |                |                |
|                |                | estimates. See |                |                |
|                |                | documentation. |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -t TRIM        | Optional       | Number of      | 1              | -t 2           |
|                |                | samples to     |                |                |
|                |                | trim. See      |                |                |
|                |                | documentation. |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -r REP         | Optional       | How to handle  | Sum            | -r Mean        |
|                |                | replicates     |                |                |
|                |                | read-counts:   |                |                |
|                |                | 'Sum' or       |                |                |
|                |                | 'Mean'.        |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -iN IGNOREN    | Optional       | Ignore TAs     | 5              | -iN 0          |
|                |                | occuring at X% |                |                |
|                |                | of the N       |                |                |
|                |                | terminus.      |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -iC IGNOREC    | Optional       | Ignore TAs     | 5              | -iC 10         |
|                |                | occuring at X% |                |                |
|                |                | of the C       |                |                |
|                |                | terminus.      |                |                |
+----------------+----------------+----------------+----------------+----------------+



::

    python PATH/src/transit.py gumbel genomes/H37Rv.prot_table data/glycerol_reads_rep1.wig,data/glycerol_reads_rep2.wig test_console_gumbel.dat -s 20000 -b 1000




|

Tn5 Gaps
~~~~~~~~

To run the Tn5 Gaps analysis from the command line, type "python
PATH/src/transit.py tn5gaps" followed by the following arguments:

Argument Type Description Default Example annotation Required Path to
annotation file in .prot_table format genomes/Salmonella-
Ty2.prot_table control_files Required Comma-separated list of paths to
the \*.wig replicate datasets
data/salmonella_2122_rep1.wig,data/salmonella_2122_rep2.wig
output_file Required Name of the output file with the results.
results/test_console_tn5gaps.dat -m MINREAD Optional Smallest read-
count considered to be an insertion. 1 -m 2 -r REP Optional How to
handle replicates read-counts: 'Sum' or 'Mean'. Sum -r Sum

Example Tn5 Gaps command:

::

    python PATH/src/transit.py tn5gaps genomes/Salmonella-Ty2.prot_table data/salmonella_2122_rep1.wig,data/salmonella_2122_rep2.wig results/test_console_tn5gaps.dat -m 2 -r Sum





Example HMM command:

::

    python PATH/src/transit.py hmm genomes/H37Rv.prot_table data/glycerol_reads_rep1.wig,data/glycerol_reads_rep2.wig test_console_hmm.dat -r Sum


| 

Resampling
~~~~~~~~~~

To run the Resampling analysis from the command line, type "python
PATH/src/transit.py resampling" followed by the following arguments:

+----------------+----------------+----------------+----------------+----------------+
| Argument       | Type           | Description    | Default        | Example        |
+================+================+================+================+================+
| annotation     | Required       | Path to        |                | genomes/H37Rv. |
|                |                | annotation     |                | prot\_table    |
|                |                | file in        |                |                |
|                |                | .prot\_table   |                |                |
|                |                | format         |                |                |
+----------------+----------------+----------------+----------------+----------------+
| control\_files | Required       | Comma-separate |                | data/glycerol\ |
|                |                | d              |                | _reads\_rep1.w |
|                |                | list of paths  |                | ig,data/glycer |
|                |                | to the \*.wig  |                | ol\_reads\_rep |
|                |                | replicate      |                | 2.wig          |
|                |                | datasets for   |                |                |
|                |                | the control    |                |                |
|                |                | condition      |                |                |
+----------------+----------------+----------------+----------------+----------------+
| exp\_files     | Required       | Comma-separate |                | data/cholester |
|                |                | d              |                | ol\_reads\_rep |
|                |                | list of paths  |                | 1.wig,data/cho |
|                |                | to the \*.wig  |                | lesterol\_read |
|                |                | replicate      |                | s\_rep2.wig    |
|                |                | datasets for   |                |                |
|                |                | the            |                |                |
|                |                | experimental   |                |                |
|                |                | condition      |                |                |
+----------------+----------------+----------------+----------------+----------------+
| output\_file   | Required       | Name of the    |                | results/gumbel |
|                |                | output file    |                | \_glycerol.dat |
|                |                | with the       |                |                |
|                |                | results.       |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -s SAMPLES     | Optional       | Number of      | 10000          | -s 5000        |
|                |                | permutations   |                |                |
|                |                | performed.     |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -H             | Optional       | Creates        | Not set        | -H             |
|                |                | histograms of  |                |                |
|                |                | the            |                |                |
|                |                | permutations   |                |                |
|                |                | for all genes. |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -a             | Optional       | Performs       | Not set        | -a             |
|                |                | adaptive       |                |                |
|                |                | appoximation   |                |                |
|                |                | to resampling. |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -N             | Optional       | Select which   | nzmean         | -N nzmean      |
|                |                | normalizing    |                |                |
|                |                | procedure to   |                |                |
|                |                | use. Can       |                |                |
|                |                | choose between |                |                |
|                |                | 'TTR',         |                |                |
|                |                | 'nzmean',      |                |                |
|                |                | 'totreads',    |                |                |
|                |                | 'zinfnb',      |                |                |
|                |                | 'betageom',    |                |                |
|                |                | and 'nonorm'.  |                |                |
|                |                | See the        |                |                |
|                |                | parameters     |                |                |
|                |                | section for    |                |                |
|                |                | the            |                |                |
|                |                | `Re-sampling   |                |                |
|                |                | method <http:/ |                |                |
|                |                | /saclab.tamu.e |                |                |
|                |                | du/essentialit |                |                |
|                |                | y/transit/tran |                |                |
|                |                | sit.html#resam |                |                |
|                |                | pling>`__      |                |                |
|                |                | for a          |                |                |
|                |                | description of |                |                |
|                |                | these          |                |                |
|                |                | normalization  |                |                |
|                |                | options.       |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -iN IGNOREN    | Optional       | Ignore TAs     | 5              | -iN 0          |
|                |                | occuring at X% |                |                |
|                |                | of the N       |                |                |
|                |                | terminus.      |                |                |
+----------------+----------------+----------------+----------------+----------------+
| -iC IGNOREC    | Optional       | Ignore TAs     | 5              | -iC 10         |
|                |                | occuring at X% |                |                |
|                |                | of the C       |                |                |
|                |                | terminus.      |                |                |
+----------------+----------------+----------------+----------------+----------------+

Example Resampling command:

::

    python PATH/src/transit.py resampling genomes/H37Rv.prot_table data/glycerol_reads_rep1.wig,data/glycerol_reads_rep2.wig data/cholesterol_reads_rep1.wig,data/cholesterol_reads_rep2.wig,data/cholesterol_reads_rep3.wig test_console_resampling.dat -H -s 10000 -N nzmean


