User Guide

Getting started

• Make sure you have Java jre 1.7 or newer installed. Note: OpenJDK "9-Ubuntu" has issues with autoupdate.
• BasePlayer can be updated automatically at File->Update or manually by downloading BasePlayer.jar from http://baseplayer.fi/update/
• Download BasePlayer and unzip it to any location with enough hard-disk space (e.g. for human studies, the reference genome size is ~3GB)
• Click Launcher.jar (in unix you need jar-launcher and Launcher.jar must have executable rights.) Alternatively click BasePlayer.jar (may not allocate enough memory for the software)
• If nothing happens, go to console/shell/command prompt and to your BasePlayer directory. Type: java -Xmx1200m -jar BasePlayer.jar
• Download preferred reference genome and its annotation from the links in the Welcome screen (opened after first start or from help menu). You can add other genomes by inserting fasta and gff3 files from the File->Change/add genome menu.
• You can allocate more memory for BasePlayer by changing MemoryLimit value in config.txt. e.g. MemoryLimit=1200m -> MemoryLimit=4G. Use Launcher.jar to apply the change.

Basic Navigation

Basic navigation tutorial can be viewed here