Here we will lay out our pipeline for inferring neoepitopes in cancer.
Steps
- Create a direcdory “mkdir NeoepitopePrediction”
- Download the IEDB tool from http://tools.iedb.org/mhci/download/
- untar the folder
tar -xvf IEDB_MHC_I-2.15.1.tar.gz - Configure the tool
cd mhc_i; ./configure - Change directory to exit IEDB folder
cd .. - Clone the github source code -
git clone https://github.com/WilsonSayresLab/Neoepitope_Prediction.git - Add all the peptide files to the respective peptide folder 15mers, 17mers, 19mers and 21mers in the downloaded git folder.
- Add hlas to the hla folder
- Run the epitopeHunter.py by -
python epitopeHunter.py.