- Use deseq2 for RNA-seq
- Use diffbind for ATAC-seq/ChIP-seq
Heatmap of differentially expressed genes
- one for transient
- one for stably expressed
- "Spark Plots" via Andrew
Upset plot of differentially expressed genes between conditions
Pathway analysis
- Use differentially expressed genes as gene set
- Use KEGG or GREAT
Rerun ATAC, ChIP pipelines
- Bug caused only 2 out of 3 comparisons to occur, so needed to rerun
Do extra ChIP samples
HPV11-E6
HPV11 E6 ChIP samples failed QC and needed to be rerun new:
- E008876
- E008877
-E008878
replaces:
- E007126
- E007127
- E007128