Tools for analysis allele specific expression in RNA-Seq data?

[saran.ela123]

Hi all !!!

I am working on arabidopsis thaliana rna seq data. i need to analysis allele specific expression of it. can any body help me to select tool for snp calling and analysis (Allele specific expression).

Thanks in advance

[dpryan]

There are a number of tools out there for this sort of thing. For SNP calling, there's GATK or samtools, but also see this recent paper that's one of the few out there to directly look at calling SNPs from RNAseq data. Once you have the SNPs, you again have a few options. Among the published tools (I think most of us have just written our own solutions, it's pretty straight-forward) are AlleleSeq and Allim.