Bioconductor packages for short read analysis- An Overview

In this lecture, Nicolas Delhomme describes the Bioconductor packages available for short read analysis. He provides an introduction to the various applications of these packages, covers what are the issues of the technologies that are commonly used in next generation sequencing and walks users through a typical workflow in the analysis of next generation sequencing data.

The workflow will cover:

  • quality assessment of the data;
  • alignment of short reads to the reference genome;
  • pre-processing of the data;
  • working with the relevant annotation for your data;
  • determine a table of counts (for RNA-Seq) or peaks (for ChIP-Seq);
  • export and visualise the results.

Notes

The code used by Nicolas during this lecture can be found here

In order to run this code you will need to install some of the following Bioconductor packages in your R session: