evaluate

Table of contents

1. Introduction
2. Input and Output
   1. Input
   2. Output
3. Usage Examples
4. Parameters

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Introduction

The evaluate command in VAMPIRE is designed to evaluate the quality of annotation.

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Input and Output

Input

Input	Format	Description	Default
Annotation	TSV	Detailed annotation results from anno command	None
Motif	TSV	Statistics of detected motifs from anno command	None

Output

Output	Format	Description	Default
Distance Matrix (raw, merged)	PDF	Distance matrix (raw values, merged direction)	None
Distance Matrix (raw, separate)	PDF	Distance matrix (raw values, separate direction)	None
Distance Matrix (normalized, merged)	PDF	Distance matrix (normalized values, merged direction)	None
Distance Matrix (normalized, separate)	PDF	Distance matrix (normalized values, separate direction)	None
Distance Matrix (raw, merged)	TSV	Distance matrix (raw values, merged direction)	None
Distance Matrix (raw, separate)	TSV	Distance matrix (raw values, separate direction)	None
Distance Matrix (normalized, merged)	TSV	Distance matrix (normalized values, merged direction)	None
Distance Matrix (normalized, separate)	TSV	Distance matrix (normalized values, separate direction)	None

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Usage Examples

vampire evaluate -t 30 evaluate annotation_prefix output_prefix

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Parameters