[BioC] FRiP for ChIP-seq in Bioconductor?

Giuseppe Gallone giuseppe.gallone at dpag.ox.ac.uk
Tue Nov 5 16:31:10 CET 2013


Ben

the SPOT quality metric, used for the ENCODE publications, probably 
allows you to obtain something very similar to the FRiP.

http://www.uwencode.org/proj/hotspot/

and

http://www.uwencode.org/data/quality

Regards
Giuseppe

On 05/11/2013 14:19, Sidders, Benjamin wrote:
> Hi All,
>
> It has been recommended for ChIP-seq experiments that the fraction of reads in peaks (FRiP) stat is a good QC measure [http://genome.cshlp.org/content/22/9/1813.full].  I can't seem to find a BioConductor package in which this is implemented – has anyone got any suggestions (other than rolling my own!)?
>
> --
> Dr Ben Sidders
> @sidderb
>
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