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

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 > > _______________________________________________ > 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 >

Ben- The DiffBind package computes a version of this after counting reads. It shows up as the "SN" value, which stands for Signal-Noise but is computed as the percentage of library reads that overlap with consensus peaks. -Rory > 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 [[alternative HTML version deleted]]