Enhance tutorial with peptide annotation and queries #6516
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Add peptide annotation and querying steps for weak and strong neopeptides.
Added details about the iPepGen workflow outputs and integration with pVACbind software for neoantigen identification. Included a disclaimer regarding workflow input validation.
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Added a disclaimer regarding workflow failures and input verification.
Added a disclaimer regarding workflow failures and input verification.
…flows/main_workflow.ga
…rkflow.ga to main_workflow.ga
…rkflows/main_workflow.ga
…flows/main_workflow.ga
Added a disclaimer regarding workflow failures and input verification.
…workflows/main_workflow.ga
Added a disclaimer about input file verification for workflow failures.
Updated text formatting procedures for assembly-derived and SAV peptides to clarify processing steps and ensure accurate integration. Removed redundant merging section and refined explanations for clarity.
subinamehta
reviewed
Nov 26, 2025
| ## Editing SAV Annotation Columns Using Column Regex Find and Replace | ||
| The **Column Regex Find and Replace** tool is used in this step to clean and standardize SAV (Single Amino-acid Variant) annotation fields. SAV entries often begin with prefixes such as `SNV_` or `INDEL_`, which must be reformatted to a consistent delimiter-based structure (`SNV|`, `INDEL|`) to be compatible with downstream peptide-annotation tools such as PepPointer. This formatting step ensures that SAV annotations can later be merged accurately with assembly-derived peptides, despite their inherently different annotation structures. | ||
| The **Column Regex Find and Replace** tool is used in this step to clean and standardize SAV (Single Amino-acid Variant) annotation fields. SAV entries often begin with prefixes such as `SNV_` or `INDEL_`, which must be reformatted to a consistent delimiter-based structure (`SNV|`, `INDEL|`) to be compatible with downstream peptide-annotation tools such as PepPointer. |
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The Column Regex Find and Replace tool is used in this step to clean and standardize SAV (Single Amino-acid Variant) annotation fields. SAV entries often begin with prefixes such as SAV_ or INDEL_, which must be reformatted to a consistent delimiter-based structure (SAV|, INDEL|) to be compatible with downstream peptide-annotation tools such as PepPointer.
Updated disclaimer section to improve clarity and formatting.
Refactor tutorial for neoantigen variant annotation to improve clarity and organization. Update sections on extracting peptides, converting coordinates, and integrating with PepPointer.
Updated disclaimer section to use comment formatting.
Updated disclaimer section to use comment formatting.
Updated disclaimer section to a comment format for clarity.
Added a disclaimer regarding workflow failures and input verification.
Updated disclaimer section to use comment format.
…flows/main_workflow.ga
Added a disclaimer about input file verification before troubleshooting workflow issues.
Updated workflow instructions for clarity and added a step for searching workflows.
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Update peptide annotation and querying steps for weak and strong neopeptides.
Add disclaimers for workflow errors and troubleshooting