Do we need replicates for PSI calculation in SUPPA2?

Question

[sreelekha]

Hi,

I don't have replicates for my RNA-seq experiment. However, I have 6 samples and six controls from different plants. I am trying to perform Alternative splicing analysis and have generated All splicing events using SUPPA2 event generator. However, I am not able to calculate PSI from individual TPM values. What should I do?

[Eric Lim]

Have your tried psiPerEvent? https://github.com/comprna/SUPPA#psi-per-local-event

[sreelekha]

Thank you for the link. Yes! I got the psi values but I guess differential expression and clustering cannot happen without PSI values.