You can also download portable version of Digenome-seq!

To download and run Digenome-seq, please follow below instructions.

Requirement

• pypy(http://pypy.org/)
• pysam(https://pypi.python.org/pypi/pysam)
• cmake(https://cmake.org/)
• g++
• git(https://git-scm.com/)


• Download Digenome-seq here(https://github.com/ibscge/digenome-toolkit2/archive/master.zip) or its source code is accessible on Github(https://github.com/ibscge/digenome-toolkit2).

STEP 1

In order to find start/end positions of aligned sequences, 1.find_position_bam.cpp needs to be compiled into binary. By running build_find_position_bam.sh , it will firstly automatically download and compile bamtools library (https://github.com/pezmaster31/bamtools) and secondly compile 1.find_position_bam.cpp into binary. To build bamtools library properly, cmake, g++, and git should be pre-installed.

STEP 2

Set an environment variable 'DIGENOME_HOME', to the directory which contains python files and executables.

STEP 3

Copy digenome-run script to bin directory (i.e. ~/bin), and run the script to analyze BAM file, as below:

STEP 4 - Usage

Before running digenome-seq, please type digenome-run -h or --help for help message.

It will automatically execute all required processes. It needs 'pysam' python package and 'pypy' to run properly.

STEP 5 - Usage for advanced users

You can start from any intermediate step to the last step. For example, if you want to run step 5~10, type command:

Additionally, you can download the source code of each step in Github(https://github.com/ibscge/digenome-toolkit2).