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coverageCount - Online in the Cloud

Run coverageCount in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command coverageCount that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


coverageCount - counting the coverage of mapped reads at each location on the entire
reference genome

DESCRIPTION


coverageCount Version 1.5.0-p1

This program calculates the coverage of mapped reads at each location on

the reference genome. It generates a binary file for each chromosome by concatenating the
coverage levels as 4-bytes integer numbers.

Usage

coverageCount [options] -i <input_file> -o <output_prefix>

Required arguments:

-i <string>
Name of input file in SAM or BAM format.

-o <string>
Prefix of the output files. Each output file contains Four-byte integer numbers

Optional arguments:

--maxMOp <int> Maximum number of 'M' operations allowed in a CIGAR string.

10 by default. Both 'X' and '=' are treated as 'M' and adjacent 'M' operations are
merged in the CIGAR string.

coverageCount Version 1.5.0-p1

This program calculates the coverage of mapped reads at each location on

the reference genome. It generates a binary file for each chromosome by concatenating the
coverage levels as 4-bytes integer numbers.

Usage

coverageCount [options] -i <input_file> -o <output_prefix>

Required arguments:

-i <string>
Name of input file in SAM or BAM format.

-o <string>
Prefix of the output files. Each output file contains Four-byte integer numbers

Optional arguments:

--maxMOp <int> Maximum number of 'M' operations allowed in a CIGAR string.

10 by default. Both 'X' and '=' are treated as 'M' and adjacent 'M' operations are
merged in the CIGAR string.

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