Pipeline for ASE (allele specific expression) using competitive alignment to diploid genome
Below are the steps by step guide to do ASE analyses using diploid genome
Step 01: Alignment on haploid genome to preparation of VCF file
This step can be done using GATK pipeline or any other pipelines of your interest. I am not going to talk about this in detail.
Step 02: Preparation of phased genotype/variants
In this step we prepare the phased variants ; but in contrary to full genome wide phased genome which are prepared using GW/CW (genome wide, chromosome wide) phasing tool, we rather run a ReadBackPhasing using VCF and BAM files. My choice of RBphasing is phaser ... weblink ?? The detailed method to prepare extended haplotype block is detailed in phase extender link ?? and phase stitcher link?? . phase stitcher is exclusively for F1 hybrids, but can apply to other hybrids depending on the relationship between input sample and collection of samples.
Step 03: Preparation of full diploid genome
Step 04: Alignment to diploid genome and transcriptome using rnaSTAR
Step 05: quantification of reads
Step 06: ASE analyses
use deepTools for descriptive summary of the alignment data: https://github.com/deeptools/deepTools/tree/develop
PCA analyese for genes of interest - http://deeptools.readthedocs.io/en/latest/content/tools/plotPCA.html