Various statistical packages are available in R and Bioconductor to perform analysis of RNA-Seq and ChIP-Seq data, focusing on the post-alignment analysis steps.

A typical workflow in the analysis of next generation sequencing data includes:

  • 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;
  • determining a table of counts (for RNA-Seq) or peaks (for ChIP-Seq) for downstream analysis; 
  • visualising the data.