Difference between revisions of "Augustus"

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==protein profiling in blocks==
 
==protein profiling in blocks==
  
augustus provides '''--proteinprofile''', '''--predictionStart''' and '''-predictionEnd''' for this, and can be used in the following manner:
+
augustus provides '''--proteinprofile''', '''--predictionStart''' and '''--predictionEnd''' for this, and can be used in the following manner:
  
 
  augustus --proteinprofile=example/prfl/BUSCO_7.prfl --predictionStart=163394 --predictionEnd=174110 --species=fly "sampleasroo2_.temp"
 
  augustus --proteinprofile=example/prfl/BUSCO_7.prfl --predictionStart=163394 --predictionEnd=174110 --species=fly "sampleasroo2_.temp"

Latest revision as of 14:35, 27 July 2016

Introduction

Worthy gene prediction program from Mario Stanke at Greifenswald.

Contents

Augustus has many script available, and several executables besides the main "augustus" executable.

It also has a config directory available through the environmental variable $AUGUSTUS_CONFIG_PATH

Usage

protein profiling in blocks

augustus provides --proteinprofile, --predictionStart and --predictionEnd for this, and can be used in the following manner:

augustus --proteinprofile=example/prfl/BUSCO_7.prfl --predictionStart=163394 --predictionEnd=174110 --species=fly "sampleasroo2_.temp"


Admin notes only

Compilation

Is a simple "make" but the Makefiles (especially the ne inside "src") need heavy editing.

filterBam particularly

colamd, got rid of this.