TaBSAP ## Targeted Bisulfite Sequencing Analysis Pipeline¶
User Guide - v1.0.2 A pipeline to analyze the data obtained from targeted bisulfite sequencing through the ion-torrent platform.¶
TaBSAP is a pipeline to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step and enables a researcher to analyze the methylation levels of their samples straight away. It’s main features are:
-Bisulfite mapping and methylation calling in one single step
-Supports single-end read alignments
-Alignment seed length, number of mismatches etc. are adjustable
-The output gives heatmap with categories.
Minimum System Requirements¶
Project Name: TaBS-Pipe¶
Project Homepage: https://github.com/pradyumnasagar/TaBSAP¶
Operating System: 64 bit Unix-like OS/ Linux Distributions(Ubuntu, CentOS, RHEL,etc.),Windows (with cygwin and R in cygwin).¶
Programming Language: SHELL Scripting.¶
Recommended System Requirement: 4GB RAM, 64 bit unix/linux OS.¶
Other Requirements: R, Pheatmap package for R,fastx toolkit(for 32 bit System ), Dos2Unix.¶
License: MIT License.¶
Installation:¶
Install the requirements Download the pipeline or clone the Pipeline in your Linux system with git Open Terminal
To download¶
wget https://github.com/pradyumnasagar/TaBSAP/archive/v1.0.2.zip
unzip v1.0.2.zip
cd v1.0.2
To Clone¶
git clone https://github.com/pradyumnasagar/TaBSAP.git
cd TaBSAP
Copy all the fastq files to fastq folder and Unconverted reference to reference folder Run the pipeline and follow the ON-Screen Instructions ./start.sh