Package for generating and analyzing transcription networks
Coltron is an application designed to build transcriptional regulatory networks.
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 firstname.lastname@example.org 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.
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.
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]
-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
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.