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Raw

Wellcome Centre for Anti-Infectives Research Logo

Raw QC

A quick way to QC .raw files from Thermo Fisher Scientific

QC example


The app produces a plot that visualizes the total ion current and cycle time vs the retention time

Running the Docker App

The mtinti/raw_qc Docker container provides a convenient solution for accessing Thermo Fisher Scientific's RAW files on Linux systems. Leveraging the ThermoFisher Scientific RawFileReader library and the Mono framework, this containerized application offers a seamless way to interact with and process RAW file data without the need for native Windows dependencies.

This guide will walk you through the steps needed to run the raw_qc Docker application on your local machine.
This app processes RAW files and requires you to provide a path to the RAW file you wish to process.

Prerequisites

  • Docker installed on your local machine.
    If you don't have Docker installed, follow the installation instructions for your platform on the Docker website.

Step 1: Pull the Docker Image

Open a terminal and pull the mtinti/raw_qc image from Docker Hub:

docker pull mtinti/raw_qc

Step 2: Prepare Your Data

Ensure that the RAW file you want to process is accessible on your local machine.
Note the full path to the directory containing this file, as you will need it in the next step.

Step 3: Run the Docker Container

Use the docker run command to start a container from the mtinti/raw_qc image.
You'll need to mount the directory containing your RAW file to the container and specify the path to the RAW file inside the container.

  • Replace /path/to/local/directory with the full path to the directory on your host machine that contains the RAW file.
  • Replace your_raw_file.raw with the name of your RAW file.
docker run --rm -v /path/to/local/directory:/data mtinti/raw_qc /data/your_raw_file.raw

This command will process the specified RAW file and output the results. The --rm flag ensures that the container is automatically removed after it exits, keeping your system clean.

Step 4: Accessing the Results

The output files will be saved in the same directory as your input RAW file on your local machine.

Troubleshooting

  • For problems related to the mtinti/raw_qc, please submit an issue in the GitHub repository.