DOKK / manpages / debian 12 / subread / qualityScores.1.en
QUALITYSCORES(1) User Commands QUALITYSCORES(1)

qualityScores - toolkit for processing next-gen sequencing data

qualityScore Version 2.0.1

Retrieve Phred score for read bases

Usage:

./qualityScores [options] -i <input_file> -o <output_file>

Required arguments:

Name of input file including read data. The default format is Fastq.
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.

Input file is in BAM format.
Input file is in SAM format.
Use only first reads in paired-end data. Only applicable for paired-end BAM/SAM input.
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.


This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.

March 2021 qualityScores 2.0.1