Getting started

Usage

Run the bamutils, bedutils, fastqutils, or gtfutils scripts. These are the main driver scripts for NGSUtils. These scripts setup the virtualenv environment and run the requested command.

For ease of use, it is recommended that you add bamutils, bedutils, fastqutils, and gtfutils to your $PATH.

Running bamutils (or the others) without any arguments will return a list of commands available. Running bamutils command will give you the parameters required for that command (or bedutils, etc…)

General usage format:

bamutils command {options} filename

bedutils command {options} filename 

fastqutils command {options} filename

gtfutils command {options} filename

For more information see the individual module documentation: * bamutils * bedutils * fastqutils * gtfutils