Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Venue:
Level 7 Seminar Room 2, WEHI1

16 October 2018

Rsubread for alternative splicing analysis

Wei Shi
WEHI Bioinformatics

RNA sequencing (RNA-seq) technologies enable expression of genes to be measured at a single nucleotide level. This high resolution provides an unprecedented opportunity to discover alternative splicing events that may occur during a biological process, such as cell differentiation or response to the loss of a master regulator. However, existing methods for detecting such events have unsatisfactory performance due to their computational inefficiency or low accuracy.

In this talk, I will describe how to use Rsubread to obtain read counts for exons and exon-exon junctions and then use these counts to discover exons and exon-exon junctions that are differently utilized in different conditions. Rsubread is a Bioconductor R package that includes multiple sequence data analysis tools such as read mapping and counting. I will show that Rsubread is much more efficient than competing tools in the quantification of exons and junctions. I will also show the result of using simulation data to compare the accuracy of Rsubread against other methods. I will finish the talk by presenting the result of using Rsubread to detect alternative splicing induced by the deletion of CIS gene in mouse natural killer cells.



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