NAME

       qualityScores - retrieve Phred score for read bases

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.

       qualityScore Version 2.0.0

              Retrieve Phred score for read bases