Calculating number of reads needed for certain coverage

• These are some useful references:

Ref1 for estimates of the number of reads required for single nucleotide variant calling: ​http://www.ncbi.nlm.nih.gov/pubmed/21771779/

Ref2 for estimates of the number of reads required for single nucleotide variant calling: ​http://www.ncbi.nlm.nih.gov/pubmed/24434847

For estimates of the number of reads required for RNA-seq and ChIP-seq experiments: ​http://www.ncbi.nlm.nih.gov/pubmed/24434847/

• Example 1

For a 3e+9 nt genome if we want 35x coverage we would need:

3e+9 * 35 / 40 = 2.625e+09 = 2.6 billion 40-nt reads
or
3e+9 * 35 / 100 = 1.05e+09 = 1 billion 100-nt reads

• Example 2

For an RNA_seq experiment: If we have 6 million paired end reads and a genome with ~7000 genes expressed X 5741 bp average gene length = 40,187,000. That is 40 mill nt to cover.

6M reads x 70 bp (35 pb per paired end reads) = 420 mill bp that we will cover.
420 mill nt that we will cover/ 40 mill nt to cover ~ 10 x coverage.