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.