SAGE tools

These tools are written to create the appropriate files for the SAGE pipeline. Note that these tools are already implemented in the pipeline.

SageCountFastq

To open the help menu:

biopet tool SageCreateLibrary -h
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

To open the help menu:

biopet tool SageCreateLibrary -h
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

To open the help menu:

biopet tool SageCreateTagCounts -h
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>