[BioC] FDR and Estimated Fragment length
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?
> -- output of sessionInfo():
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