Biological Sequence Analysis

⚠️ TOP-OF-MIND RULE: Trimmomatic "reads completely discarded" = F + R + 2*D, summed across samples

When a question asks about Trimmomatic "reads completely discarded" / "reads thrown out" / "reads not in any output", do NOT report the Dropped field alone. Dropped counts PAIRS where both mates failed; each pair = 2 individual reads. Plus the Forward-only and Reverse-only buckets also discard one read per pair.

reads_discarded = sum over samples of (Forward_Only + Reverse_Only + 2 * Dropped)

❌ WRONG: sum(Dropped per sample) — typically reports ~thousands, GT is 100×+ higher

✅ RIGHT: sum(F + R + 2*D per sample)

Full counter table is in the FASTQ section below.