Targeted Bisulfite Sequencing Analysis Pipeline
User Guide - v0.0.2
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
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.
Install the requirements
Download the pipeline or clone the Pipeline in your Linux system with git
git clone https://github.com/pradyumnasagar/TaBSAP.git
Copy all the fastq files to
fastqfolder and Unconverted reference to
Run the pipeline and follow the