coltron 1.0.2

Package for generating and analyzing transcription networks

Overview

Coltron is an application designed to build transcriptional regulatory networks.

Installation

Installation of Coltron has only been vetted on Ubuntu 12.04 LTS and Ubuntu 14.04 LTS. If you encounter any errors in the installation process, please contact [e-mail] for additional help.

Confirm PIP Installation:

pip --version
pip 1.5.6 from /usr/local/lib/python2.7/dist-packages/pip-1.5.6-py2.7.egg (python 2.7)

If the pip –version command generates a command not found error, you will have to download PIP. Instructions for the installation can be found at the following location.

Run the following command to start the module download:

$ sudo pip install coltron

This command should produce output that looks like this:

$ sudo pip install coltron
  Downloading coltron-1.0.1.tar.gz (8.8MB)
  100% |████████████████████████████████| 8.8MB 7.3kB/s
  Building wheels for collected packages: coltron
      Running setup.py bdist_wheel for coltron
      Stored in directory: /home/name/.cache/pip/wheels/83/8c/26/def2b761371d20e93848a6628662df
  Successfully built coltron
  Installing collected packages: coltron
  Successfully installed coltron-1.0.1

Once the PIP installation is complete, the data files that Coltron uses to operate must be downloaded.

Data Download

Coltron provides a command for downloading its required files. The command can be executed as follows:

$ sudo coltron-get-data

The required data is downloaded from the web and stored in Coltron’s data repository. This process can be time consuming.

Usage

The following command is used to run the main Coltron executable:

$ coltron [options] -e [ENHANCER_FILE] -b [BAM_FILE] -g [GENOME] -o [OUTPUTFOLDER] -n [NAME]

Options:

-h HELP, --help            show this help message and exit
-e ENHANCERS, --enhancer_file=ENHANCERS
                      Provide a ROSE generated enhancer table
                      (_AllEnhancers.table.txt)
-b BAM, --bam=BAM     Provide a bam that corresponds to the super enhancer
                      table
-g GENOME, --genome=GENOME
                      Provide the build of the genome to be used for the
                      analysis. Currently supports HG19, HG18 and MM9
-o OUTPUT, --output=OUTPUT
                      Enter an output folder
-n NAME, --name=NAME  Provide a name for the job
-s SUBPEAKS, --subpeaks=SUBPEAKS
                      Enter a BED file of regions to search for motifs
-x EXPCUTOFF, --expCutoff=EXPCUTOFF
                      Enter the expression cutoff to be used to define
                      candidate TFs
-l EXTENSION, --extension-length=EXTENSION
                      Enter the length to extend subpeak regions for motif
                      finding
-a ACTIVITY, --activity=ACTIVITY
                      A table with refseq in the first column and activity
                      (expression or promoter acetylation) in second
-E ENUMBER, --enhancer_number=ENUMBER
                      Enter the number of top ranked enhancers to include in
                      the analysis. Default is all super-enhancers
--promoter=PROMOTER   Enter True if the promoters should be included in the
                      analysis
--motifs=MOTIFS       Enter an alternative PWM file for the analysis
-t TFS, --tfs=TFS     Enter additional TFs (comma separated) to be used in
                      the bindinf analysis
-v VALLEY, --valley=VALLEY
                      Parameter for valley calling threshold, default = 0.3

Dependencies

Coltron has a number of software dependencies for full operation:

Bamliquidator – version 1.2.0

Samtools – version 0.1.19

FIMO – version 4.91

NetworkX – version 1.8.1

PIP installation will take care of the NetworkX dependency. Installation guides for the remaining dependencies can be found at the links provided.