Long-Read-Proteogenomics-Analysis

Download Reference Data

The reference data can be downloaded here

Download Results Data

To use the data used in the "Enhanced protein isoform characterization through long-read proteogenomics" manuscript download the data from this :

s3://sheynkman-lab-lifebit/deploit/users/5fa6c3c061aba10112169d7d/projects/602eb362e9e4e10112f0dd63/jobs/60bcb29b303ee601a69d8c74/

Update Config

In the config.py file, update the PIPELINE_RESULTS_DIRECTORY and REFERENCE_DIRECTORY to the paths of the two directories where the data above is downloaded

PIPELINE_RESULTS_DIRECTORY='path/to/results/directory'
REFERENCE_DIRECTORY='path/to/reference/directory'

Run Jupyter Notebooks

Within the 0_pre_analysis directory, run get_appris_reference_isoforms.py and get_number_gencode_transcripts.py

python get_appris_reference_isoforms.py  
python get_number_gencode_transcripts.py

Open each .ipynb file and run each notebook fully. Figures are stored in the /plot directory and statistics are stored in the /stats directory