QuickMIRSeq: User Guide
+How to run QuickMIRSeq pipeline from scratch
-Explore integrated and interactive report
Open the index.html file under Results folder and you will have access to all data and figures, and drill down miRNA-seq analysis results in an interactive way.

-Meaning of mouse icons
Left click to interactive plot Left click Right click Double left click Scroll middle wheel
-Create a boxplot for one gene
Step 1: Click on the "pointing hand" icon on the master report HTML page to get to gene expression table.


Step 2: Search by keyword and then left click on any column except the first two on a gene.


Step 3: Now you should see dot plot to show gene expression level in RPKM value on all samples


Step 4: Right click on any plot area to bring up the drop down menu for sample grouping, data transformation and chart customization


Step 5: Group samples by following menu "Group Samples" and then select features you want samples to be grouped upon for box plot. The sample features are gathered from the optional "sample.annotation.txt" file under "Summary" directory.


Step 6: Click on any plot area to remove the menu and you should see a boxplot.


Step 7: Data can be transformed to various scales by right click on the plot to bring up the menu and then follow "Data" -> "Transform" -> "Log Base 2" for log2 transformation


Step 8: The chart can also be customized in many ways. For example, The font of sample labels will be enlarged by following "Customize" -> "Sample Labels" -> "Font" -> "Bigger". The more you click on the "Bigger" button, the larger the font becomes.


Step 9: Add y-axis title by following "Customize" -> "Axes Titles" -> "Text". Type in title in the input box and then click the nearby cycling button.

Step 10: The size of Window and Canvas can be changed by click-and-drag the left bottom corner as indicated by the black arrows. Follow "Data Points Attributes" -> "Color by" to color data points based on a feature.


Step 11: Move mouse up to the top of the canvas to activate the top menu, click on the "Camera" button to get a nice png image for publication.


-Create a heatmap for genes
Step 1: Type in or select genes from the above table. Click on "Plot" when it is ready.


Step 2: Right click on any plot area to bring up the drop down menu for sample grouping, data transformation and chart customization


Step 3: Sort samples by following menu "Data" -> "Sort Samples" -> "By Sample Category" and then select features you want samples to be sorted. The sample features are collected from the optional "sample.annotation.txt" file during pipeline run.


Step 4: Data can be transformed to various scales by right click on the plot to bring up the menu and then follow "Data" -> "Transform" -> "Log Base 2" for log2 transformation


Step 5: The chart can be customized in many ways. For example, The font of sample labels will be enlarged by following "Customize" -> "Variable Labels" -> "Font" -> "Bigger". The more you click on the "Bigger" button, the larger the font becomes.


Step 6: The size of Window and Canvas can be changed by click-and-drag the left bottom corner as indicated by the black arrows.


Step 7: Move mouse up to the top of the canvas to activate the top menu, clicak on the "Camera" button to get a nice png image for publication.


+How to make the report publicly available at github.com
Maintained by Baohong Zhang