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.