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.
Use coverageCount online using onworks.net services
