Bioinformatics Recipe Cookbook
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Visualizing large scale genomic variations.

We call a variation large-scale when the changes do not fit into the sequence portion of a short read.

Paired-end read sequencing is then the methodology that allows us to identify where the reorganization took place. Pairs in the unexpected orientation, template sizes of unexpected lengths together can provide the necessary guidance to identify the "reorganization" junction points relative to the reference genome.

This recipe provides code that:

  1. Creates a modified genome based on the reference.
  2. Simulates sequencing reads from this modified genome
  3. Aligns the simulated reads against the reference
  4. Allow you to visualize the results in IGV


A detailed presentation that explains the steps and rationale for this recipe can be found at:

Please refer to the lecture above for links to the chapters that cover each concept.

Recipe Code
Recipe Interface
Interface Preview
Interface preview shows the resulting view of the combined interface elements.
Interface specification
Interface element specification. Shows the code and the resulting interface element.
Double click on an element to insert it into the interface.
Integer values
                        label = "Window size"
                        display = "INTEGER"
                        value = 100
                        range = [1, 100]
                        help = "Selects the smoothing window."
Float values
                        label = "P_Value Cutoff"
                        display = "FLOAT"
                        value = 0.05
                        range = [0, 1]
                        help = "Selects the cutoff."
Text box
                    label = "Run Number"
                    display = "TEXTBOX"
                    value = "SRR519926"
                    regex = 'SRR\d+'
                    help = "Please provide SRR Run number"
Dropdown menu
                    label = "Select color"
                    display = "DROPDOWN"
                    choices = [ ["R","Red"], ["B","Blue"] ]
                    value = "R"
                    help = "Select a color of your choice"
Check box
                    label = "Cross Validate"
                    display = "CHECKBOX"
                    value = true
                    help = "Apply cross validation on the results."
Upload Field
                    label = "Upload a file "
                    display = "UPLOAD"
                    help = "Upload a file to analyze"
Pick Data
                    label = "Pick data"
                    source = "PROJECT"
                    help = "Pick data from this project."
Radio Buttons
                    label = "Select species"
                    display = "RADIO"
                    choices = [ ["c","Cat"], ["d","Dog"] ]
                    value = "c"
                    help = "Select the species."
Edit Recipe
Recipe display name
Unique identifier for the recipe.

Determines who can run a recipe.

A detailed explanation of what the recipe does (markdown OK).
Image :
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Used to order recipes (optional).

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