Welcome to SNAF’s documentation!

Splicing Neo-Antigen Finder (SNAF) is an easy-to-use pipeline to predict MHC-bound neoantigens (T-antigen) and altered surface protein (B-antigen) produced by abnormal alternative splicing events from RNA-Seq data.

Content

• Installation
  • Step 1: AltAnalyze
  • Step 2: SNAF
  • Step 3: Reference Dataset
  • Step 4: (Optional) Install netMHCpan4.1 and TMHMM2.0
  • Testing installation
• Tutorial
  • Running AltAnalyze to identify alternative splicing events
  • Identify MHC-bound neoantigens (T-antigen)
  • Identify altered surface proteins (B-antigen)
  • Compatibility (Gene Symbol & chromsome Coordinates & Genome Version)
• Development
  • NeoJunction Class
  • JunctionCountMatrixQuery Class
  • SurfaceAntigen Class
• API
  • MHC bound peptides (T antigen)
  • Interface to proteomics
  • Surface Antigen (B antigen)
  • GTEx Viewer (tumor specificity)
  • Miscellaneous
• Troubleshooting
  • 1. Singularity Error
  • 2. AltAnalyze warnings and errors
  • 3. How to do HLA genotyping?
  • 4. AltAnalyze steps take too long
  • 5. Recommended alignment workflow
  • 6. Running MaxQuant in Linux
  • 7. How to interpret T antigen output?
• Change Log
  • Version SNAF.git: e23ce39512a1a7f58c74e59b4b7cedc89248b908 (2024.01.15)
  • Version 0.7.0 (2023.05.23)
  • Version 0.6.0 (2022.07.11)
  • Version 0.5.2 (2022.04.17)
  • Version 0.5.1 (2022.04.16)
  • Version 0.5.0 (2022.04.06)
  • Prior to Version 0.5.0
• Contact