IMPROVEMENTS.md

Improvements and Consistency Fixes

This repository copy was improved without changing the original source repository.

Inconsistencies identified

• Project folder names were inconsistent (TWASTutorial, TWAStutorial, TWAS_tutorial).
• Several commands assumed folders existed but did not create them with mkdir -p.
• kallisto module command used ml load instead of ml (inconsistent with other sections).
• samples.trimmed.txt creation was shown as a commented line but later required by Slurm.
• R plotting section used fread() without loading data.table.
• Multiple typos and wording issues reduced clarity (for example: "cromosomes", "specie", "copy pase").
• downloadSamples.sh lacked a shebang, error handling, and output-directory creation.

Improvements applied

• Rewrote README.md for consistency, clearer sequencing, and reproducibility.
• Standardized working directory naming (TWAS_tutorial) and path usage.
• Added explicit mkdir -p and setup/verification commands.
• Corrected module-loading and script snippets for FastQC, Trimmomatic, and Kallisto.
• Added missing library(data.table) in the Manhattan plot section.
• Modernized downloadSamples.sh with:
  • #!/usr/bin/env bash
  • set -euo pipefail
  • automatic output directory creation
  • loop-based URL download for easier maintenance

Scope

• No biological assumptions or model choices were changed.
• No original data files were modified.