diff --git a/AUTHORS.rst b/AUTHORS.rst index 751b588..3938d09 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -10,6 +10,11 @@ Development Lead * Thorsten Bischler Contributors ------------- +============ + ++----------------+------------------------------------------------------+ +| Name | GitHub Username | ++================+======================================================+ +| Kaneez Rubab | `@RubabBhatti `_ | ++----------------+------------------------------------------------------+ -None yet. Why not be the first? diff --git a/docs/source/index.rst b/docs/source/index.rst index d170fb2..4b60c61 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -13,7 +13,8 @@ Table of content example_analysis troubleshooting license - versions + versions + Visualization READemption in a nutshell ========================= diff --git a/docs/source/visualization.rst b/docs/source/visualization.rst new file mode 100644 index 0000000..95adff7 --- /dev/null +++ b/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-.sh + $ ./IGB-linux-amd64-.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. + +