<commit_before># GIVE Tutorial 3: Use GIVE-Toolbox to manage data tracks 

**Table of Contents**
---------
* [Introduction](#introduction)  
* [Walkthrough Example](#walkthrough-example)
    * [Step 1: Deployment of GIVE](#step-1-deployment-of-give)
    * [Step 2: Initialization and Create Reference Genome](#step-2-initialization-and-create-reference-genome) 
    * [Step 3: Create Track Groups](#step-3-create-track-groups)
    * [Step 4: Create Gene Annotation Track](#step-4-create-gene-annotation-track)
    * [Step 5: Create Data Track from bed File](#step-5-create-data-track-from-bed-file)
    * [Step 6: Create Data Track from bigWig File](#step-6-create-data-track-from-bigwig-file)
    * [Step 7: Create Data Track from interaction File](#step-7-create-data-track-from-interaction-file)
    * [List and Remove Data Tracks](#list-and-remove-data-tracks)
    * [Using The Customized GIVE Genome Browser](#using-the-customized-give-genome-browser)


## Introduction
The current version of GIVE needs MySQL for managing back end data source. It might be complicated for users who are not familiar with MySQL to build data tracks from their own data. So we integrated all the back end operations into a bundle of shell(bash) script tools, which is GIVE-Toolbox. GIVE-Toolbox greatly simplifies the operations for configuring and initializing the data source, as well as building and managing data tracks. Here is a walk-through example, you will learn how to build a customized genome browser from zero just in 7 steps. It has never been easier!

If you would like to know the actual operations in MySQL, please refer to [GIVE manual 3.2: MySQL commands for managing data in GIVE data source](../manuals/3.2-dataSource.md).

GIVE support `UCSC gene table`, `bed`, `bigWig` and `interaction` format data tracks. Here are some documents of the format definitions and related visualizing options in GIVE: 
- [`UCSC gene table` format](https://genome.ucsc.edu/cgi-bin/hgTables): knownGene annotation files can be download from UCSC Genome Browser (GENCODE track) 
- [`bed` Tracks](../manuals/4.1-bed.md)
- [`bigWig` Tracks](../manuals/4.2-bigwig.md)
- [`interaction` Tracks](../manuals/4.3-interaction.md)
<commit_msg>Grammar fixes<commit_after># GIVE Tutorial 3: Use GIVE-Toolbox to manage data tracks 

**Table of Contents**
---------
* [Introduction](#introduction)  
* [Walkthrough Example](#walkthrough-example)
    * [Step 1: Deployment of GIVE](#step-1-deployment-of-give)
    * [Step 2: Initialization and Create Reference Genome](#step-2-initialization-and-create-reference-genome) 
    * [Step 3: Create Track Groups](#step-3-create-track-groups)
    * [Step 4: Create Gene Annotation Track](#step-4-create-gene-annotation-track)
    * [Step 5: Create Data Track from bed File](#step-5-create-data-track-from-bed-file)
    * [Step 6: Create Data Track from bigWig File](#step-6-create-data-track-from-bigwig-file)
    * [Step 7: Create Data Track from interaction File](#step-7-create-data-track-from-interaction-file)
    * [List and Remove Data Tracks](#list-and-remove-data-tracks)
    * [Using The Customized GIVE Genome Browser](#using-the-customized-give-genome-browser)


## Introduction
The current version of GIVE needs MySQL for managing back end data sources. It might be complicated for users who are not familiar with MySQL to build data tracks from their own data. Therefore, we integrated all the back end operations into a bundle of shell(bash) script tools, which is GIVE-Toolbox. GIVE-Toolbox greatly simplifies the operations for configuring and initializing data sources, as well as building and managing data tracks. Here is a walk-through example, you will learn how to build a customized genome browser from zero just in 7 steps. It has never been easier!

If you would like to know the actual operations in MySQL, please refer to [GIVE manual 3.2: MySQL commands for managing data in GIVE data source](../manuals/3.2-dataSource.md).

GIVE support `UCSC gene table`, `bed`, `bigWig` and `interaction` format data tracks. Here are some documents regarding the format definitions and related visualizing options in GIVE: 
- [`UCSC gene table` format](https://genome.ucsc.edu/cgi-bin/hgTables): knownGene annotation files can be download from UCSC Genome Browser (GENCODE track) 
- [`bed` Tracks](../manuals/4.1-bed.md)
- [`bigWig` Tracks](../manuals/4.2-bigwig.md)
- [`interaction` Tracks](../manuals/4.3-interaction.md)

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