Get counts for allele specific expression analysis

Question

[Picasa]

Hi all,

I am looking for your help about tools/pipeline for allele specific expression analysis. From various papers, I have come up with this pipeline:

1) Call variant with GATK using WGS samples

2) Create 2 transcriptomes using these variants and my annotation: so I have one transcriptome for allele 1 and one transcriptome for allele 2

3) Map my RNA-seq data against this pool transcriptome using bowtie2

4) and get count with ASE-TIGAR (http://nagasakilab.csml.org/ase-tigar/) per gene per haplotype

5) Perform downstream analysis with DEseq2.

It works and I got some results but I am wondering if you know any other tools than ASE-TIGAR to get the counts just for comparison/validation purpose.

Also, if you have other pipeline recommendation, I would be happy to hear ! Thanks for your help.

[grant.hovhannisyan]

For the part of DESeq2, I would recommend having a look at this page http://rpubs.com/mikelove/ase

[Picasa]

Thanks for your link. Do you have experience with ASE study ?

[grant.hovhannisyan]

a bit, though the field itself is just emerging with no well-accepted standards.

[Kristoffer Vitting-Seerup]

You could take a look at this quantification tool