.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH QUALITYSCORES "1" "February 2020" "qualityScores 2.0.0+dfsg-1~bpo10+1" "User Commands"
.SH NAME
qualityScores \- retrieve Phred score for read bases
.SH USAGE
.PP
qualityScores [options] \fB\-i\fR <input_file> \fB\-o\fR <output_file>
.PP
Required arguments:
.TP
\fB\-i\fR <string>
Name of input file including read data. The default format is
Fastq.
.TP
\fB\-o\fR <string>
Name of output file that is a text file including Phred scores
for each read base.
.PP
Optional arguments:
.HP
\fB\-\-gzFASTQinput\fR Input file is in gzipped Fastq format.
.TP
\fB\-\-BAMinput\fR
Input file is in BAM format.
.TP
\fB\-\-SAMinput\fR
Input file is in SAM format.
.TP
\fB\-\-first\-end\fR
Use only first reads in paired\-end data. Only applicable for
paired\-end BAM/SAM input.
.TP
\fB\-\-second\-end\fR
Use only second reads in paired\-end data. Only applicable for
paired\-end BAM/SAM input.
.HP
\fB\-\-counted\-reads\fR <int> Total number of reads to be extracted from the input
.IP
file. 10,000 by default.
.HP
\fB\-\-phred\-offset\fR <33|64> refer to subread aligner.
.PP
qualityScore Version 2.0.0
.IP
Retrieve Phred score for read bases
.PP