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TOGA2

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preprocessing

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Yury V. Malovichko edited this page May 5, 2026 · 1 revision

Warning

This page is under development

Wiki pages Pages 30

Home
alignment
Automated input generation with "prepare‐input" mode
Chain artefact resolution
classification
Computing CDS integrity statistics
Exon annotation
feature_extraction
gene_inference
Glossary
Inactivating mutations
Input files
Installation
Logging & troubleshooting
logs
Loss status classification
meta
nextflow
Output structure
Parallel execution
preprocessing
Query projection & gene notation
Rejection reasons
SpliceAI prediction generation with “spliceai" mode
SpliceAI‐aware TOGA2
tmp
toga2orthogroups
Top level files
ucsc_browser_files
Using SpliceAI predictions with TOGA2

Contents

Start page
Installation
Input files
- Automated input generation with "prepare‐input" mode
- SpliceAI prediction generation with “spliceai" mode
Pipeline description
Using SpliceAI predictions with TOGA2
Output description
- Top level files
- meta
- logs
- tmp
- nextflow
- ucsc_browser_files
Interpreting TOGA2 results
- Query projection & gene notation
- Rejection reasons
Logging & troubleshooting
Glossary

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