Lesson 1: The Omics Hierarchy and File Architecture

Biological context: the omics layers

Omics refers to technologies used to study large-scale molecular information in biological systems. A common view follows the central dogma of molecular biology.

• Genomics (DNA-Seq)
  • Studies the complete DNA blueprint and sequence variation such as SNPs
• Transcriptomics (RNA-Seq)
  • Studies expressed RNA transcripts and which genes are active under specific conditions

Technical definitions: the big four file formats

FASTQ: raw sequence reads

FASTQ is the raw output from sequencing platforms such as Illumina and Oxford Nanopore.

• Definition: text format that stores biological sequences and per-base quality scores
• 4-line structure per read:
  • Line 1: header, starts with @
  • Line 2: sequence (A, C, T, G, N)
  • Line 3: separator, starts with +
  • Line 4: quality string (Phred scores encoded as ASCII characters)

FASTA: reference sequence

FASTA is a simple format for nucleotide or protein sequences.

• Definition: sequence format used for references and assembled contigs
• Structure: entry header starts with > followed by sequence lines

SAM/BAM: alignment records

SAM/BAM represent alignments of reads to a reference.

• SAM: human-readable alignment text format
• BAM: compressed binary version of SAM for efficient storage and processing
• Practical rule: store and process BAM, inspect with tools such as samtools view

VCF: variant calls

VCF stores sequence variants relative to a reference.

• Definition: tab-delimited format for genomic variants
• Typical fields include chromosome, position, reference allele, and alternate allele

Hands-on conceptual exercise

Inspect raw FASTQ structure in your training data.

cd ~/Training/short_reads/unpaired
zcat SRR11282408_Healthy.fastq.gz | head -n 4

Line 4 contains quality symbols that encode base-call confidence. Higher-quality symbols correspond to lower error probability.