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Old 08-02-2014, 05:06 PM   #18
Bioinformatics Engineer
Location: University of Cambridge, UK

Join Date: Jun 2010
Posts: 14

HI albireo,

The package CexoR is also available from Bioconductor for ChIP-exo peak calling (

Pedro M

Originally Posted by albireo View Post
Hi, yes that is what I meant. I have performed a number of FRiP analyses (similarly to what done in the 2012 ENCODE Genome Research ChIP-seq methods paper) with very disappointing results in one case (~4-5% FRiP). This data is decent in other respects (high correlation of replicates, consensus motif present in 70% of the peaks).

I have not tested this specific peak caller, but have some experience with other methods, including Genetrack (the original peak caller used in the Pugh publication), Macs 2.0, Apex, Peakzilla and GEM, with wildly varying results. I should also add that my data is Illumina-based and was processed directly by Peconic.
Pedro Madrigal
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