logo

Table of contents

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

Introduction

The logo command in VAMPIRE is designed to analyze and visualize the motif variation. It can plot sequence LOGO in three types – count, probability and information based on motif file or annotation file.

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
Base Counts TSV Counts of A/T/C/G/- for each loci None
Base Counts PDF/PNG Seq logo in count None
Base Probability PDF/PNG Seq logo in probability None
Base Information PDF/PNG Seq logo in information None

Usage Examples 

vampire logo -t motif -f pdf annotation_prefix output_prefix

Parameters