Hello, 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. -Ryan 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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor