From 6e22f736f7961ea571b523b2543313aeeb3c3b52 Mon Sep 17 00:00:00 2001 From: RubabBhatti Date: Thu, 24 Jul 2025 15:59:49 +0500 Subject: [PATCH 1/8] Adding visualization guide for RNA-seq data --- docs/source/visualization.rst | 55 +++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 docs/source/visualization.rst diff --git a/docs/source/visualization.rst b/docs/source/visualization.rst new file mode 100644 index 0000000..f3896fc --- /dev/null +++ b/docs/source/visualization.rst @@ -0,0 +1,55 @@ +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 named as + "READemption_analysis/output/salmonella_coverage-tnoar_mil_normalized/" and "READemption_analysis/output/salmonella_coverage-tnoar_min_normalized/", + you can use either file but for IGB visualization "READemption_analysis/output/salmonella_coverage-tnoar_mil_normalized/" + is recommended for clear display of normalised expressions. + + +Additional Tips +--------------- + +1. You can change the color of the strands of reference genome, gff3 or wiggles file data by +locating the track in IGB main window where there is a table like view named as "Data management view" +, Click on the color appearing in the boc below "FG". +2. IGB only support file formats like ".fasta", ".gff3", ".bigwig", ".bam", ".bed", ".wig", ".vcf". Make +sure you load the right file format. +3. Verify your files are compatible with IGB's version. + From 40df6716b1c333f0ab0af78b45781c664dde89c1 Mon Sep 17 00:00:00 2001 From: RubabBhatti Date: Thu, 24 Jul 2025 16:32:50 +0500 Subject: [PATCH 2/8] Add visualization guide for RNA-seq data --- docs/source/visualization.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/visualization.rst b/docs/source/visualization.rst index f3896fc..951c31b 100644 --- a/docs/source/visualization.rst +++ b/docs/source/visualization.rst @@ -49,7 +49,9 @@ Additional Tips 1. You can change the color of the strands of reference genome, gff3 or wiggles file data by locating the track in IGB main window where there is a table like view named as "Data management view" , Click on the color appearing in the boc below "FG". + 2. IGB only support file formats like ".fasta", ".gff3", ".bigwig", ".bam", ".bed", ".wig", ".vcf". Make sure you load the right file format. + 3. Verify your files are compatible with IGB's version. From 43935b1dd3d75c68070033fd9fdc78fe835f1ffb Mon Sep 17 00:00:00 2001 From: RubabBhatti Date: Thu, 24 Jul 2025 16:50:17 +0500 Subject: [PATCH 3/8] Adding visualization guide for RNA-seq data --- docs/source/visualization.rst | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/source/visualization.rst b/docs/source/visualization.rst index 951c31b..b956525 100644 --- a/docs/source/visualization.rst +++ b/docs/source/visualization.rst @@ -48,10 +48,8 @@ Additional Tips 1. You can change the color of the strands of reference genome, gff3 or wiggles file data by locating the track in IGB main window where there is a table like view named as "Data management view" -, Click on the color appearing in the boc below "FG". - +, Click on the color appearing in the boc below "FG". 2. IGB only support file formats like ".fasta", ".gff3", ".bigwig", ".bam", ".bed", ".wig", ".vcf". Make -sure you load the right file format. - +sure you load the right file format. 3. Verify your files are compatible with IGB's version. From 622241703e8d999357aa68436cbf2e42d76409d2 Mon Sep 17 00:00:00 2001 From: RubabBhatti Date: Thu, 24 Jul 2025 16:51:57 +0500 Subject: [PATCH 4/8] Adding visualization guide for RNA-seq data --- docs/source/visualization.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/visualization.rst b/docs/source/visualization.rst index b956525..f317922 100644 --- a/docs/source/visualization.rst +++ b/docs/source/visualization.rst @@ -49,7 +49,9 @@ Additional Tips 1. You can change the color of the strands of reference genome, gff3 or wiggles file data by locating the track in IGB main window where there is a table like view named as "Data management view" , Click on the color appearing in the boc below "FG". + 2. IGB only support file formats like ".fasta", ".gff3", ".bigwig", ".bam", ".bed", ".wig", ".vcf". Make sure you load the right file format. + 3. Verify your files are compatible with IGB's version. From c7694d8150d5b891e845aaa6826bd54861505ebd Mon Sep 17 00:00:00 2001 From: RubabBhatti Date: Thu, 24 Jul 2025 16:58:00 +0500 Subject: [PATCH 5/8] Adding visualization guide for RNA-seq data --- docs/source/visualization.rst | 30 ++++++++++++++++++------------ 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/docs/source/visualization.rst b/docs/source/visualization.rst index f317922..95adff7 100644 --- a/docs/source/visualization.rst +++ b/docs/source/visualization.rst @@ -37,21 +37,27 @@ Load the data in IGB 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 named as - "READemption_analysis/output/salmonella_coverage-tnoar_mil_normalized/" and "READemption_analysis/output/salmonella_coverage-tnoar_min_normalized/", - you can use either file but for IGB visualization "READemption_analysis/output/salmonella_coverage-tnoar_mil_normalized/" - is recommended for clear display of normalised expressions. +NOTE +==== +After running `READemption_analysis`, you will get two folders of coverage: -Additional Tips ---------------- +- `READemption_analysis/output/salmonella_coverage-tnoar_mil_normalized/` +- `READemption_analysis/output/salmonella_coverage-tnoar_min_normalized/` -1. You can change the color of the strands of reference genome, gff3 or wiggles file data by -locating the track in IGB main window where there is a table like view named as "Data management view" -, Click on the color appearing in the boc below "FG". +You can use either of these folders for visualization, but for IGB display, the following is **recommended** for a clearer view of normalized expressions: -2. IGB only support file formats like ".fasta", ".gff3", ".bigwig", ".bam", ".bed", ".wig", ".vcf". Make -sure you load the right file format. +- `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. -3. Verify your files are compatible with IGB's version. From a7473c1377ab535fda8c51df3bcd67883849db32 Mon Sep 17 00:00:00 2001 From: RubabBhatti Date: Thu, 24 Jul 2025 17:06:54 +0500 Subject: [PATCH 6/8] Added visualization.rst to index.rst --- docs/source/index.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 ========================= From 344d6bd851fcdc4556a3a8b249b33e6eb597cae3 Mon Sep 17 00:00:00 2001 From: RubabBhatti Date: Thu, 24 Jul 2025 18:26:13 +0500 Subject: [PATCH 7/8] Added myself as a contributor --- AUTHORS.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/AUTHORS.rst b/AUTHORS.rst index 751b588..206f9ba 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -10,6 +10,8 @@ Development Lead * Thorsten Bischler Contributors ------------- +============ -None yet. Why not be the first? +| Name | GitHub Username | +|--------------|------------------------------------------------------| +| Kaneez Rubab | [@RubabBhatti](https://github.com/RubabBhatti) | From 1ed3c10dfdc0c205b03182dbd569f832f3c91164 Mon Sep 17 00:00:00 2001 From: RubabBhatti Date: Thu, 24 Jul 2025 18:29:06 +0500 Subject: [PATCH 8/8] Added myself as a contributor --- AUTHORS.rst | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/AUTHORS.rst b/AUTHORS.rst index 206f9ba..3938d09 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -12,6 +12,9 @@ Development Lead Contributors ============ -| Name | GitHub Username | -|--------------|------------------------------------------------------| -| Kaneez Rubab | [@RubabBhatti](https://github.com/RubabBhatti) | ++----------------+------------------------------------------------------+ +| Name | GitHub Username | ++================+======================================================+ +| Kaneez Rubab | `@RubabBhatti `_ | ++----------------+------------------------------------------------------+ +