BioMicroCenter:CoverageCalculations: Difference between revisions
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(New page: {{BioMicroCenter}} ==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. The Illum...) |
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==Determining ideal read length and depth of coverage== | ==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. | 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. <BR><BR> | ||
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: | |||
{| border=1 | |||
|Species | |||
|Length | |||
|- | |||
|E coli | |||
|4 Mbp | |||
|- | |||
|S.cerevisiae | |||
|12.5Mbp | |||
|- | |||
|C.elegans / Drosophila | |||
|100-150Mbp | |||
|- | |||
|Human / Mouse / Rat | |||
|3Gbp | |||
|} |
Latest revision as of 19:21, 10 January 2013
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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 |