Team-WA1

Meet-EU Team WA1

Topic A : Prediction of TADs

How to download repo? (Linux / MacOS)

1. Create GitHub account
2. Provide email to get access.
3. Create ssh key

• cd /home/my-user/.ssh
• ssh-keygen -t rsa -b 4096
• provide name and optional password
• cat <given-name>.pub
• copy retrieved
• GitHub settings
• SSH and GCP keys tab
• add ssh key
• type any name
• paste result of cat-a
• navigate to terminal
• ssh -T [email protected] -i ~/.ssh/<given-name>
• now I can:
• git clone [email protected]:<scope-user>/<project-name>.git, in our case git clone [email protected]:meet-eu-21/Team-WA1.git

Data description:

1. HiC - data to our algorithms
2. TAD - additional metadata + results

Downloading data:

1. All (approx. 25 gb) - ./scripts/download_all.sh
2. Only GM12878 (approx. 11 gb) - ./scripts/download_GM12878.sh

Run:

1. install python3
2. install required packages
3. download and unpack data (can use scripts directory)
4. in src directory python3 main.py {args} (available args and their behaviour can be found in summary_report.pdf)

• example: python3 main.py--results-path=../results --resolution=100k --data-path=../data/www.lcqb.upmc.fr/meetu/dataforstudent/HiC/GM12878/100kb_resolution_intrachromosomal --run-topdom=True --with-metrics-results=True --with-results-coordinates=True --topdom-sensitivity=0.04 --topdom-window-size=5 --chromosomes=1,22,X

Results:

1. Results should be available in {desired directory}/topdom / {desired directory}/arrowhead directory
2. Remember to change resolution if you change data