What is RAD-seq (and its variants)

The goal is to attain a
reduced representation of the genome

Sequence to higher coverage by selecting fewer genomic regions.

Concentrate sequencing to the same regions across all samples.

Multiplex many samples onto a sequencing run.

Variant methods differ in cost and selectivity

Concerns about RAD-seq

Why not just sequence the whole genome at low-coverage?

Many genomes are very large, so it remains too expensive,
especially when studying many samples/pops/species.

Low coverage base calling can estimate population-wide
statistics well, but not individual level.

Low coverage is messy/difficult for extracting loci
for individuals (e.g., for phylogenetics) b/c so much missing data.

RAD-seq has a lot of missing data

Variation in the presence/absence of a restriction
cut site can cause loci to be present in some samples but not others.

Compared to many other methods (e.g., transcriptomes, UCEs) RAD-seq still
provides substantially more data (e.g., SNPs). The important concern is how your analysis tools deal with missing information.

Allele dropout can affect base calls

Many genomes are very large, so it remains too expensive,
especially when studying many samples/pops/species.

Low coverage base calling can estimate population-wide
statistics well, but not individual level.

Low coverage is messy/difficult for extracting loci
for individuals (e.g., for phylogenetics) b/c so much missing data.

A quick introduction to the command line

Lines starting with hash (#) are only comments

  # This is the general format of unix command line tools
  $ program -option1 -option2 target
        

  # e.g., the 'pwd' program with no option or target prints your cur dir
  $ pwd
        

I'll use a grey background to show the returned value

    /home/deren/        

The ipyrad command line interface

We'll cover this soon in the RADcamp tutorial.

  # The ipyrad CLI can be used in a terminal
  $ ipyrad -p params-data.txt -s 123 -t 4 -c 16 
        

Hierarchical File System

Always know where you are and where your files are.

  # The root (top) of the entire filesystem (used for writing full paths).
  $ /

  # Here, in my current directory (used for writing relative paths).
  $ ./

  # Up one directory from my current directory (a relative path).
  $ ../
        

Hierarchical File System

Always know where you are and where your files are.

  # show the files and folders in a location (default target is cur dir)
  $ ls 

  # show result as a list for cur dir.
  $ ls -l ./

  # show another location on the filesystem
  $ ls -l /bin/

  # move to a new location. This becomes your new cur dir.
  $ cd folder/
        

Your location (current directory) starts from / (the root) and is described by a nested set of directory names leading to your location.

  # use 'pwd' program with no option or target to ask where am I now?
  $ pwd
        

    /home/deren/        

We can make new directories and change our location.

  # make a new directory (mkdir is the program, genomics is the target)
  $ mkdir genomics

  # change directory (move) into the new directory and run pwd again
  $ cd genomics
  $ pwd
        

    /home/deren/genomics