Is anyone aware of software or algorithms that test for differential allele-specific expression between groups (obviously conditional on being heterozygous at the locus in question)?
I didn't get your question completely. But can't you call for ASE genes for control and the treatment group and then select the differential ASE list or you are looking for some sophisticated statistical methods. Alleleseq is a tool to call for ASE genes. Link : http://alleleseq.gersteinlab.org/
I am aware of this ALEA is a computational toolbox for allele-specific (AS) epigenomics analysis.
never tried by myself though..
Did you manage to find one ?
I believe ASARP is another option:
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