TSSprediction from RNAseq

Date

2025-08-04

Project Description

TSS prediction based solely on RNAseq data. Using ML methods (NN+gLM) to embed and predict data.

Project Organization

The project is organized in the following directories:

• src/: scripts that are connected to a GitHub repo
• data/: raw data, cleaned data, etc.
• analysis/: scripts that are not connected to a GitHub repo
• figures/: plots, graphs, etc.
• playground/: for testing purposes
• results/: results of the project

Project Team

• Student: Arthur Neumann
• Supervisor: Maik Wolfram-Schauerte + Mathias Witte Paz

CLI Documentation

Top-Level Commands

• data
  Data-related operations. Contains subcommands for cleaning, viewing, and windowing datasets.

• train No current implementation, planned for future ML implementations

Subcommands under data

1. clean

• Cleans the raw dataset and outputs processed files.
• Usage Example:

  python3 main.py data clean

2. view

• Previews cleaned or raw datasets in the terminal, with options to save a preview.
• Options:
  • --dataset {Master,Clean}: Choose which dataset to view (Master for raw, Clean for processed). Default: Clean.
  • --rows <int>: Number of rows to preview. Default: 5000.
  • --save <path>: Save the preview to a .tsv file at the specified path.
• Usage Example:

  python3 main.py data view --dataset Clean --rows 1000 --save /path/to/save

3. window

• Performs window-based analysis on the cleaned dataset.
• Options:
  • --size <int>: Window size in each direction from TSS. Default: 1000.
  • --conds <list>: List of conditions to filter by. Default: Control. Choices: Control, nov, rif, tet
  • --strand {+, -, master, all}: Specify strand for windowing. Default: all.
  • --preview <path>: [ Optional ] Path to save preview output.
  • --wiggle_f <path>: [ Optional ] Path to forward wiggle file.
  • --wiggle_b <path>: [ Optional ] Path to backward wiggle file.
  • --output_dir <path>: Output directory for results.
• Usage Example:

  python3 main.py data window --size 1000 --conds Control nov --strand + --preview /path/to/preview