PCA for multiple transcriptome-assemblies

Question

[Shahzad]

Hi Can we perform Principal component analysis PCA for multiple transcriptome-assemblies to show the shared similarity between them?

[sangram_keshari]

Yes, you can plot a PCA on the normalized read-count or expression data of the transcriptome-assemblies.

[Kevin Blighe]

What exact input data do you have? - just the assembled transcript sequences in FASTA format?

[harshraje19]

I have gene count data for PCA analysis, can you suggest the pipeline in R for the PCA analysis

[sangram_keshari]

In R you can simply Principal Components Analysis

pca <- prcomp(read_count_df)

For plotting

library(ggfortify)  
autoplot(pca, loadings.label = TRUE)