Biological Sequence Analysis ⚠️ TOP-OF-MIND RULE: Trimmomatic "reads completely discarded" = , summed across samples When a question asks about Trimmomatic "reads completely discarded" / "reads thrown out" / "reads not in any output", do NOT report the field alone. 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. ❌ WRONG: — typically reports thousands, GT is 100×+ higher ✅ RIGHT: Full counter table is in the FASTQ section below. --- RULE ZERO — Check for pre-computed results FIRST Before follow…