1. Galaxy – https://useg Set up your account

2. Galaxy – Two ways to get your data

3. Galaxy – the data you will need for this lab

4. Galaxy – two datasets (four files)

5. Galaxy – import the data

6. Galaxy – create “history”

7. NGS Toolbox

8. NGS - QC

9. NGS - Alignment

11. NGS Toolbox

12. TOPHAT2

13. CuffLinks

14. CuffDiff You can figure out …

15. Visualization Visualization function in Galaxy IGV (trick – keep zooming in)

16. Lab description 1.Compare the gene expression profiles obtained using paired-end RNA- seq between two epithelial cell lines – the breast tumor cell line MCF7 and a non-tumor cell line MCF10A 2.Report the list of significantly differentially expressed (DE) genes between the two cell lines and identify the enriched GO terms and pathways (if any), provide a possible biological explanation 3.Provide visualization (screen capture or save figure) for two highly significant DE genes. 4.Do you observe any gene which is NOT differentially expressed by has a CDS (coding region) that is differentially expressed? 5.The data we use is highly downsampled. Given what you see about this data, what you would expect for the significant DE genes in the original data? Would you expect to see more? 6.Pick another pair of cell lines and compare. Report the 2 – 4.