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Targeted Bisulfite Sequencing Analysis Pipeline
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fastq
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0.autonames.sh
1.autoQuality.sh
10.autorenameFasta.sh
11.biqref.sh
12.biq.sh
13.postbiq.sh
15.resfile.sh
16.percent.sh
17.heatmap.sh
2.automap.sh
3.autounmappedReads.sh
4.autounconverted.sh
5.autorcconverted.sh
6.autorcunconverted.sh
7.autoconvert2fasta.sh
8.autoextractGeneFasta.sh
9.automergeFasta.sh
LICENSE
README.md
_config.yml
heatmap.R
heatmapcat.R
image.png
no.txt
old.12.biq.sh
requirement
run.sh
run4server.sh
start.sh
testglist.sh
welcome

README.md

TaBSAP

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

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:

  1. Install the requirements

  2. 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

  1. Copy all the fastq files to fastq folder and Unconverted reference to reference folder

  2. Run the pipeline and follow the ON-Screen Instructions

./start.sh

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