quality-scores

name	quality-scores
description	Use when sampling per-base Phred quality values from FASTQ, gzipped FASTQ, BAM, or SAM files via the Subread `qualityScores` utility.
disable-model-invocation	true
user-invocable	true

quality-scores

Quick Start

• Command: qualityScores -i input.fastq -o output.txt
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/qualityScores
• Version observed locally: 2.1.1
• Output shape: one comma-separated quality vector per sampled read

When To Use This Tool

• Extract raw per-base Phred values from sequencing files for lightweight QC or downstream summaries.
• Sample qualities from plain FASTQ, gzipped FASTQ, BAM, or SAM input.
• Restrict quality extraction to first-end or second-end reads from paired BAM / SAM files.
• Keep using Subread's small helper instead of writing a one-off parser.

Common Patterns

# 1) Plain FASTQ input
qualityScores -i reads.fastq -o qualities.txt

# 2) Gzipped FASTQ input
qualityScores --gzFASTQinput -i reads.fastq.gz -o qualities.txt

# 3) BAM input, first mates only, with a smaller sample
qualityScores \
  --BAMinput \
  --first-end \
  --counted-reads 2000 \
  -i alignments.bam \
  -o qualities.txt

Recommended Workflow

1. Pick the correct input-mode flag: none for plain FASTQ, --gzFASTQinput, --BAMinput, or --SAMinput as needed.
2. Set --counted-reads deliberately if the default sample of 10000 reads is too large or too small.
3. Run the command and inspect the output text file to confirm the expected per-read comma-separated quality values.
4. If using BAM or SAM, apply --first-end or --second-end only when you really want one mate subset.

Guardrails

• The skill folder is quality-scores, but the real executable is qualityScores.
• Both -i and -o are required.
• The tool does not implement clean help switches: --help and -h print an unrecognized-option message and then fall through to usage text.
• Default input interpretation is plain FASTQ; BAM and SAM require explicit mode flags.
• --first-end and --second-end are only meaningful for paired BAM / SAM input.
• FASTQ Phred encoding can be adjusted with --phred-offset 33|64; for SAM / BAM data, scores are usually already Phred+33.