We recently got RNAseq data from out F1 heterozygotes (plants). The goal is to identify allele specific expression differences for putative and unknown candidates by aligning to Ref-genome.
If you only want to find the expression difference, then you can use STAR (https://code.google.com/p/rna-star/) for alignment (which is quick, but require a long of computer memory), then run HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) and DESeq (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html) for the differential expression result.
However, both Tophat-cufflink pipeline and the one I mentioned above will not account for the allele specific expression. There is a similar question on biostar and you might be interested to have a look:
https://www.biostars.org/p/83283/
https://www.biostars.org/p/59118/
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