RNA-seq data analysis, a practical approach

You can download supporting material such as R code examples, data files and Chipster sessions here.

These analysis sessions were made using the freely available Chipster software. You can open Chipster and visualize the result files using username guest, password guest. Note that you should not unzip the session files prior to loading them to Chipster. You can find more example sessions by selecting "Open example session" in Chipster.

• Differential gene expression analysis using HTSeq, DESeq2 and edgeR
• Differential exon expression analysis using DEXSeq

• Reads 1 for GM12892 replicate 2 (fastq) used in chapters 3, 4 and 6.
• Reads 2 for GM12892 replicate 2 (fastq) used in chapters 3, 4 and 6.
• Chromosome 18 reads 1 for GM12892 replicate 2 (fastq) used for assembly in chapter 5.
• Chromosome 18 reads 2 for GM12892 replicate 2 (fastq) used for assembly in chapter 5.
• A zip file containing exon level read count tables for chapter 9.
• A zip file containing data and miRDeep2 protocol for practising analysis described in chapter 13.

• A zip file containing code examples for chapters 7, 9 and 10.

• Code for extracting chromosome 18 reads (fastq) from BAM used for assembly in chapter 5.