In this practical we will be reviewing some of methods for visualising and clustering data from RNAseq data.
In todays session we will continue to review the Tissue RNAseq we were working on in our last sessions.
Preprocessed counts for Tissue data for this practical session can be found in the Data directory. Data/tissueCounts.RData
Produce a PCA plot of the GO “heart development” genes. You can check QuickGO webbsite to find its ID
Create a Heatmap of all genes and include row annotation showing members of heart development, liver development and kidney development GO set.
Import the replicated peaks for H3k27ac and H3K4me3 for Heart tissue samples found in Data directory. Identify genes with both H3k4me3 and H3k27ac peaks in their TSS (+/-500bp).
H3k4me3 = Data//ENCFF599BFW.bed.gz
H3k27ac = Data//ENCFF733HUI.bed.gz
Create a heatmap of the top 100 marker (both positive and negative) for PC1 and add annotation for genes with H3k27ac and H3K4me3 peaks in their TSS.