Sex Determination in a Fish
Background
Aquaculture production has become increasingly important to satisfy seafood and fishery product demands. Researcher wants to develop genomic resources to improve sustainable domestic aquaculture. They recently assembled and annotated a genome and now want to collect wild fish to explore genetic diversity in local populations and identify the sex determining region.
Ideal Experimental Design Elements
Funding for project
$X,XXXSequencing Technology
: Illumina HiSeq 3000Number of lanes
: 20 lanesLength of read
: 150bpNumber of Samples
: 90Coverage Depth
: 29xYear of Sequencing
: hypothetical 2017
Real Experimental Design Elements
Funding for project
$X,XXXSequencing Technology
: Illumina HiSeq 2500Number of lanes
: 4 lanesLength of read
: 100bpNumber of Samples
: 90Coverage Depth
: 1.9xYear of Sequencing
: 2015
Questions
How is Coverage Depth Determined?
The quick and dirty calculation is to take the read length (150) multiply by 2 if it is paired end multiply by the number of fragments the Illumina machine produces (300 Million) = 150bp * 2 * 300M = 90,000 million or 90 billion bases output from a single lane. Take that number and divide it by your genome size. If your genome size is 1 gigabase then you have approximately 90x coverage.
While this can give an approximation for coverage depth the reality is that the coverage depth at any given locus in the genome will be a distribution around this number with some regions having more and some regions having less coverage.