This is the command qualityScores 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
qualityScores - a component of subread suite
USAGE
qualityScores [options] -i <input_file> -o <output_file>
Required arguments:
-i <string>
Name of input file including read data. The default format is Fastq.
-o <string>
Name of output file that is a text file including Phred scores for each read base.
Optional arguments:
--gzFASTQinput Input file is in gzipped Fastq format.
--BAMinput
Input file is in BAM format.
--SAMinput
Input file is in SAM format.
--first-end
Use only first reads in paired-end data. Only applicable for paired-end BAM/SAM
input.
--second-end
Use only second reads in paired-end data. Only applicable for paired-end BAM/SAM
input.
--counted-reads <int> Total number of reads to be extracted from the input
file. 10,000 by default.
--phred-offset <33|64> refer to subread aligner.
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