Allele-Specific Expression (Illumina)

Question

[Yannick Wurm]

Mirroring http://www.biostars.org/post/show/905/allele-specific-gene-expression-in-ngs-454-data/ . Is there a good method/pipeline to detect allele-specific expression from Illumina RNAseq data (when you know both parental genomes?)

Cheers, Yannick