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Types of sequencing data:

Whole-genome resequencing data

• If we already have a #Reference Genome for the population/species, we can use a shorter (cheaper) sample, otherwise we need a long sample.
• In the past we needed long fragments of DNA, but now we can use shorter samples dueto new tech - this is what lets us use aDNA and hDNA.
• Used for Genome-Wide Association Study (GWAS) and population genomics

Reduced Representation (RADseq)

• Used in Quantitative Trait Locus mapping - we are only looking at a few loci in the genome
• Much cheaper

RNA sequencing

• We need very fresh tissue so its only really possible from lab samples
• Used to study gene expression.

Reference Genome

• DNA sequence that spans the whole genome of an organism
• Genes are annotated with relevant information such as gene functions known from other species

Sequence alignment

• Once we have our sample, we need to align it to the reference genome with some mapping software
• Quality control the data make sure its all good
• Look for variants like:
  • SNPs
  • Structural Variants
    • chromosonal inversions
    • insertions
    • deletions

Types of analysis:

Genome-Wide Association Study (GWAS)

Quantitative Trait Locus mapping

• This is the main topic of the lecure and practical today