BedtoolsCoverageToCounts.md 774 Bytes
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# BedtoolsCoverageToCounts

## Introduction
This tool enables a user to generate a count file, out of a coverage file.


## Example
To get the help menu:
~~~bash
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biopet tool BedtoolsCoverageToCounts -h
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Usage: BedtoolsCoverageToCounts [options]

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

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input: A coverage file produced with bedtools
output: A count file with the counts from the the values inside the coverage file. Where values could be almost everything, e.g.
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genes, ensemblIDs etc. etc.

To run the tool:
~~~bash
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biopet tool BedtoolsCoverageToCounts
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~~~