You can use this command in your terminal
/Applications/Install\ OS\ X\ El\ Capitan.app/Contents/Resources/createinstallmedia
Here the El Capitan installer must be in the application folder to do this step.
In this example, the El Capitan installer in the application folder and Myusb is the name of USB drive which is used to boot.
sudo /Applications/Install\ OS\ X\ El\ Capitan.app/Contents/Resources/createinstallmedia --volume /Volumes/MyVolume --applicationpath /Applications/Install\ OS\ X\ El\ Capitan.app