# SAGE tools


## SageCountFastq
~~~
Usage: SageCountFastq [options]

  -l <value> | --log_level <value>
        Log level
  -h | --help
        Print usage
  -v | --version
        Print version
  -I <file> | --input <file>
        
  -o <file> | --output <file>
~~~

## SageCreateLibrary
~~~
Usage: SageCreateLibrary [options]

  -l <value> | --log_level <value>
        Log level
  -h | --help
        Print usage
  -v | --version
        Print version
  -I <file> | --input <file>
        
  -o <file> | --output <file>
        
  --tag <value>
        
  --length <value>
        
  --noTagsOutput <file>
        
  --noAntiTagsOutput <file>
        
  --allGenesOutput <file>

~~~

## SageCreateTagCounts
~~~
Usage: SageCreateTagCounts [options]

  -l <value> | --log_level <value>
        Log level
  -h | --help
        Print usage
  -v | --version
        Print version
  -I <file> | --input <file>
        
  -t <file> | --tagLib <file>
        
  --countSense <file>
        
  --countAllSense <file>
        
  --countAntiSense <file>
        
  --countAllAntiSense <file>
~~~