Adding visualization guide for RNA-seq data

AUTHORS.rst

@@ -10,6 +10,11 @@ Development Lead
 * Thorsten Bischler
 
 Contributors
-------------
+============
+
++----------------+------------------------------------------------------+
+| Name           | GitHub Username                                     |
++================+======================================================+
+| Kaneez Rubab   | `@RubabBhatti <https://github.com/RubabBhatti>`_    |
++----------------+------------------------------------------------------+
 
-None yet. Why not be the first?

docs/source/index.rst

@@ -13,7 +13,8 @@ Table of content
    example_analysis
    troubleshooting
    license
-   versions	      
+   versions	
+   Visualization      
 
 READemption in a nutshell
 =========================

docs/source/visualization.rst

@@ -0,0 +1,63 @@
+Visualization of RNA-seq data
+==============================
+
+This guide explains how to visualize RNA-seq data files in integrated genome browser (IGB). 
+
+Installing IGB
+--------------
+
+1. Install IGB for your system from IGB official website: https://www.bioviz.org/ .
+2. Follow the installation requirements for Linux, Windows and macOS.
+3. Launch IGB.
+
+For linux, run the following command in terminal after installation to open IGB:
+::
+
+    $ chmod +x IGB-linux-amd64-<version>.sh
+    $ ./IGB-linux-amd64-<version>.sh
+
+
+Preparing data for visualization
+--------------------------------
+
+After running the READemption analysis, you"ll get wiggles files in coverage folder. 
+These wiggle files will be used for visualization. 
+
+1. Go to the coverage folder first.
+2. Navigate ".wig" or ".wig.gz" files of your sample.
+3. Unzip the .wig.gz files (optional) by running the following command:
+         $ Gunzip *.wig.gz
+
+Load the data in IGB
+--------------------
+
+1. Open IGB.
+2. Load reference genome file (".fa", ".fna", ".fasta") and annotation file (".gff3") by clicking on
+ "File" → "Open file" on the top left corner, and then click on "Load sequence" on top right corner next to zoom option .
+3. Load the coverage ".wig" files. 
+4. Zoom in and zoom out into the regions of your interest.
+
+NOTE
+====
+
+After running `READemption_analysis`, you will get two folders of coverage:
+
+- `READemption_analysis/output/salmonella_coverage-tnoar_mil_normalized/`
+- `READemption_analysis/output/salmonella_coverage-tnoar_min_normalized/`
+
+You can use either of these folders for visualization, but for IGB display, the following is **recommended** for a clearer view of normalized expressions:
+
+- `READemption_analysis/output/salmonella_coverage-tnoar_mil_normalized/`
+
+
+
+Tips for Visualization in IGB
+=============================
+
+1. You can change the color of the strands of the reference genome, GFF3, or wiggle file data by locating the track in the IGB main window where there is a table-like view named **Data Management View**. Click on the color appearing in the box below **FG**.
+
+2. IGB only supports file formats like `.fasta`, `.gff3`, `.bigwig`, `.bam`, `.bed`, `.wig`, and `.vcf`. Make sure you load the correct file format.
+
+3. Verify your files are compatible with your version of IGB.
+
+