Do we need replicates for PSI calculation in SUPPA2?
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8 days ago
sreelekha ▴ 10

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?

SUPPA2 splicing RNA-seq Alternative • 220 views
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Have your tried psiPerEvent? https://github.com/comprna/SUPPA#psi-per-local-event

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