[BioC] FDR and Estimated Fragment length

Ryan rct at thompsonclan.org
Sat Jan 4 00:39:37 CET 2014


You can estimate the fragment length through strand cross-correlation 
analysis. The MACS peak caller will give you an estimate of fragment 
length based on this (or possibly a similar method; I don't remember the 
precise method used). Most peak callers also allow you to specify the 
fragment length explicitly. The fragment length (or estimated fragment 
length) is used to infer the midpoint of the fragment, since the mapped 
location indicates one end of the fragment. The midpoint of the fragment 
is presumably the best indicator of the binding location of the protein.


On 12/27/13, 5:39 PM, George Harris [guest] wrote:
> Hi list
> What is the estimated fragment length in chip seq and how is this used in peak detection?
> What other files are used in calculating the false discover rate(FDR) in chip seq apart from the negative peak files?
> Thanks
> Harris
>   -- output of sessionInfo():
> None
> --
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