griffithlab / griffithlab/pVACtools
QUESTION: How to integrate netchop results to aditionnally filter possible peptides
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- Dominant language
- Python
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- 188
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Description
Hello, I would like to know your current take on integrating the clivage score in the pipeline.
I ran the downstream filtering from the all_epitopes.tsv myself, and wanted to see results from NetChop with the predicted neoantigens.
With my current experiment, it seems that most of the PASS neoantigens I obtained running the pipeline report an internal clivage site above 0.5.
It seems inacurate to just discard them all, so I wanted to know how you implemented this score in the pipeline as downstream filtering.
Thank you.
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start by reviewing the all_epitopes.tsv output and the reported NetChop cleavage scores, then trace any existing documentation or pipeline guidance for downstream filtering. Done means documenting the project's current approach to internal cleavage sites above 0.5 and explaining how users should interpret or apply the score.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100