It is invaluable as a tool for viewing and interpreting the "raw data" of many NGS data analysis pipelines. The Integrative Genomics Viewer is a program for reading several types of indexed database information, including mapped reads and variant calls, and displaying them on a reference genome. Database indexes enable one to rapidly pull specific subsets of the data from them. In order to more quickly retrieve the data we are interested in analyzing or viewing, most programs have a way of treating these data files as databases. Navigate the view of the genome and interpret the display of this data.īecause NGS datasets are very large, it is often impossible or inefficient to read them entirely into a computer's memory when searching for a specific piece of data.Load output from calling genetic variants.Load output from mapping reads to a reference genome.Create a custom genome database (usually used for microbial genomes) or load a pre-existing genome assembly (usually used for the genomes of model organisms and higher Eukaryotes).In this tutorial, we're going to learn how to do the following in IGV: The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.
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