Bioinformatics Seminar
Time:
Venue: Na
16 October 2018
NaRsubread for alternative splicing analysis
Wei ShiWEHI 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.