ASEanalysis

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# Analysis pipelines for allele specific expression (ASE) in pigs

## 1. Introduction

The utitlities for unbiased allele-specific read mapping, discovery of Parent-of-origin effect (POE) genes and Allele-genotype effect (AGE) genes and exploring the characteristics of allelic patterns in chromatin accessibility and methylation.

## 2. Analysis pipelines

This repository contains analysis pipelines for ASE in pigs, including:

- Whole-genome sequence alignment, quality control, variants calling, and individualized genome reference construction
- RNA-seq alignment, quality control, quantification, variants calling, and transcriptome annotations
- Tissue-specific gene expression and stage-specific gene expression
- POE genes and AGE genes identification
- ATAC-Seq alignment, quality control, peaks calling, and genome-wide accessiable chromoatin signal visualization
- Peaks annotation, tissue-specific and developmental stage-specific chromatin accessibility analysis
- Allele-specific chromatin accessibility analysis
- WGBS alignment, quality control, duplication removing, methylation context extracting and CpG methylation matrix generation
- Allele-specific methylation analysis

Pipeline components are public available in this repository.

## 3. System requirements
- Linux: CentOS Linux release 7.9.2009
- Python: Python 3.6.8
- Perl: Perl v5.16.3
- R: R 4.0.3

ASEanalysis

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