PCA for multiple transcriptome-assemblies

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

assembly rna-seq next-gen r

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written 6.9 years ago by Shahzad •

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

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written 6.9 years ago by sangram_keshari

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

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written 6.9 years ago by Kevin Blighe

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

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written 6.4 years ago by harshraje19 •

In R you can simply Principal Components Analysis

pca <- prcomp(read_count_df)

For plotting

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

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written 6.4 years ago by sangram_keshari

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