🧬 Arabis Genomic and Transcriptomic Scripts

This repository contains a set of scripts and pipelines for genomic and transcriptomic analysis, focused on Arabis species. It includes tools for QTL mapping, RNA-seq analysis, Stacks processing, and genome assembly quality checks.

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📄 Files Included

File Name	Description
QTLmapping.R	R script for performing QTL analysis and visualizing genotype–phenotype associations.
gstacks_distribs.R	R script to summarize and visualize read depth and SNP distributions from Stacks gstacks output.
stacks_raw_process.py	Python script for initial processing of raw reads using the Stacks pipeline.
deseq_drought_transcriptome.py	Python script for differential expression analysis using DESeq2 (via count data or R integration).
Genome_assmebly_Quality_Curation_pipeline.txt	A step-by-step protocol to assess and curate genome assembly quality. Developed using non-model plant genomes.

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🔧 Requirements

R

• tidyverse
• qtl
• ggplot2

Python 3

• pandas
• argparse
• os
• (optional) rpy2 if integrating with R

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▶️ Usage

Clone the repository:

git clone https://github.com/Abdubidopsis/Scripts.git
cd Scripts