BioMicroCenter:CoverageCalculations
From OpenWetWare
Jump to navigationJump to search
| HOME -- | SEQUENCING -- | LIBRARY PREP -- | HIGH-THROUGHPUT -- | COMPUTING -- | DATA MANAGEMENT -- | OTHER TECHNOLOGY |
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 |
