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Example of script to query BioMart, parse and create a BridgeDb database

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BioMartScript

Introduction

A script to create a BrigdeDb database from BioMart queries.

Run

In your terminal:

java -jar BioMart2BridgeDb.jar <configFile> <outputPath> <oldDB> <inclusive>

  • <configFile>: location of configuration file

  • <outputPath>: Path for the new database

  • <oldDB>: (optional) directory of the old database - run QC

  • <inclusive>: (optional) use inclusive BridgeDb list

List of default config files:

https://github.com/JonathanMELIUS/BioMartScript/tree/bc62ed7fba16dd143292ee10fb4e261d196dd7a6/src/resource

Example: Danio rerio config file

How to create your own config file

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Example of script to query BioMart, parse and create a BridgeDb database

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