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Old 05-11-2009, 10:36 PM   #11
Chema
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Location: Poznan, Poland

Join Date: Jul 2008
Posts: 6
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Hi,

In this paper, you can find other ChIP-seq algorithm. It is implemented in R
http://www.pubmedcentral.nih.gov/art...?artid=2671559

The baisc idea was
1) Extend the reads and use the minimum number of read that overlap a a nucleotide position among both strnad. This is, the number of reads should be supported by the two strands independently. This is to avoid peaks that have a block shape.
2)Normalize data and sample regarding their covarage distribution
3)Use permutation to estimate the FDR control
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