For a typical ChIP Sequencing run, what is the sequence tag length and how does that typically relate to target binding site coverage? Do you achieve at least 10X coverage?
Using Illumina sequencing, the sequence tags are typically 35 bp in length. The amount of sequence requested is 250 megabases (MB), which corresponds to 7-8 million sequences [need to check our numbers]. This amount of sequencing is now attainable using one channel in a GAII flow cell. Typically 80% of “quality-filtered” sequences (those that pass the quality criteria) will map uniquely, and the coverage at each site depends on the binding strength for the factor at that site. Coverage at a given binding site can be as many as 200 tags and most sites have at least 10X coverage (this depends on the number of tags sequenced).
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