coltron 1.0.2

概述

coltron是一个用于构建转录调控网络的应用程序。

安装

Coltron的安装只在Ubuntu12.04 LTS和Ubuntu14.04 LTS上进行过审查。如果在安装过程中遇到任何错误，请与drpolaskijr@gmail.com联系以获取其他帮助。

确认PIP安装：

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

如果pip–version命令生成一个command not found错误，则必须下载pip。安装说明可以在下面的location中找到。

运行以下命令启动模块下载：

$ sudo pip install coltron

此命令应生成如下输出：

$ 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

PIP安装完成后，必须下载Coltron用于操作的数据文件。

数据下载

coltron提供下载所需文件的命令。命令的执行如下：

$ sudo coltron-get-data

所需的数据从网上下载并存储在coltron的数据存储库中。这个过程可能很耗时。

用法

以下命令用于运行主coltron可执行文件：

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

选项：

-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

依赖关系

Coltron有许多软件依赖项可用于完全操作：

Bamliquidator–1.2.0版

Samtools –版本0.1.19

FIMO –版本4.91

NetworkX –1.8.1版

pip安装将处理networkx依赖关系。安装指南 对于其余依赖项，可以在提供的链接中找到。