Large Scale Genomic Variation

Large Scale Genomic Variation

Visualizing large scale genomic variations.

1 result • updated 5.5 years ago by Istvan Albert

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.

Copy recipe
You need write access to the project to edit.
You need write access to the original recipe to edit.
Recipe Interface Builder
Click the buttons on the right to create new fields.
Interface Editor
Edit the content of each interface element.
You need write access to the original recipe to edit.
Edit Recipe
Recipe display name
Unique identifier for the recipe.
Image :
Optional image for the recipe ( 500px Maximum ).
Used to order recipes (optional).

Insert Image


Powered by the release 2.3.6