I was wondering if someone can tell me where I can find more about how to do an allele-specific Expression (ASE) analysis using either Kallisto or different tools. I have read the description in the Kallisto paper about ASE, but didn't really understood what I need to do to enable such analysis. Do I need to run the Kallisto analysis differently than the default parameters?
In general I would like to know, if there is a good workflow/tool/description on how to do an allele-specific expression analysis with RNA-Seq data.
any help would be appreciate.