tanyaphung/neoepitope_prediction

Neoepitope Prediction

Here we will lay out our pipeline for inferring neoepitopes in cancer.

Steps

• Git clone the repo:

git clone https://github.com/tanyaphung/Neoepitope_Prediction.git

• Change working directory to Neoepitope_Prediction:

cd Neoepitope_Prediction/

• Create a conda environment

conda env create --name NeoepitopePrediction --file environment.yml

• After you create a conda environment, activate it:

conda activate NeoepitopePrediction

• Download the IEDB tool from http://tools.iedb.org/mhci/download/

• untar the folder:

tar -xzvf IEDB_MHC_I-2.19.1.tar.gz

• configure the tool and exit out of the directory

cd mhc_i/
./configure
cd ..

• You will get a message like this after configuring the tool:

All prerequisites found!
Copying the standalone-specific netMHCcons template into place
IEDB MHC class I binding prediction tools successfully installed!
Use the command 'python src/predict_binding.py' to get started

• Add peptides to respective folder.

• Note that the file format has to be "TCGA-" + patient +"_Varscan_variants_filter.pass."+ str(num) +".peptide".

• Add hla to the hla folder. Then delete the file all_hlas_here.txt.

rm -f hla/all_hlas_here.txt

• Submit job on cluster:

• Modify the script submit.sh to put in your information
• Note: because of some issue in memory, right now this will work on ASU agave cluster.