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Pipeline for ASE (allele specific expression) using competitive alignment to diploid genome

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ASE_analyses_pipeline

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

To be continued

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