Estimate allelic imbalance

Question

[sbombin]

Hello,

I am trying to estimate allelic imbalance in C.remanei. Most of the methods that I found require to have separate maternal and paternal transcriptoms to estimate allilic imbalance based on SNPs. However, I have only one combined paternal transcriptom. Does anyone know how to estimate allelic imbalance and/or genetic imprinting with only combined paternal transcriptom? Could you suggest any publications where I could find useful information or any pipelines?

Thank you

[Devon Ryan]

If you only have one transcriptome then you're pretty much SOL. The best you can do is call variants against it, but then you're going to miss any paternal-specific expression.