BioMicroCenter:CoverageCalculations

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Image:BioMicroCenter-header6.jpg

Determining ideal read length and depth of coverage

The BioMicro Center offers a wide variety of read lengths, both in single-end and paired-end formats. Often, it is useful to calculate the expected average coverage.

Coverage for genomic samples can be calculated as:

 no.reads(1/2) * readlength * no.cluster
 ---------------------------------------
             genome size 

For ChIP samples, the following modified formula can be used:

      no.reads * readlength * no.cluster
  -----------------------------------------
  no.sites * site.length / % reads in sites

Some standard genome sizes:

Species Length
E coli 4 Mbp
S.cerevisiae 12.5Mbp
C.elegans / Drosophila 100-150Mbp
Human / Mouse / Rat 3Gbp
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