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Old 11-02-2008, 11:50 PM   #1
ECO
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Location: SF Bay Area, CA, USA

Join Date: Oct 2007
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Default A brief review of recent ChIP-Seq tools literature

Seems I can't go a week without finding a paper describing a new ChIP-Seq analytical tool, so I thought it would be helpful to put together a list of a few of the most interesting papers in this area.

For those not familiar with ChIP-Seq, it involves massively parallel sequencing of nucleic acids recovered from a chromatin-immunoprecipitation (ChIP). ChIP uses an antibody to capture protein that has been previously crosslinked to DNA in its native state. Thus, ChIP-Seq allows sequencing of all DNA that a specific protein physically interacts with within the cell.


There are quite a few studies recently which describe either a software tool, and/or an analytical framework for working with this type of data. The difficulty and thus the plethora of approaches is using the read density information to "call peaks" or more precisely, statistically significant ChIP-Seq binding sites.

Recent papers I have found helpful are below, in reverse chronological order. Please accept my apologies in advance if I've missed your favorite tool.


November

October

September

August

Hopefully those are useful. I'll post up my experiences with some of these tools soon, and would love to hear yours.
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