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Old 01-27-2014, 05:32 AM   #12
Location: Europe

Join Date: Sep 2012
Posts: 39

Originally Posted by jwfoley View Post
Thanks, albireo. Just to be clear, are you saying that in the worse cases, you have a ChIP-seq-like SN ratio, i.e. there is high background throughout the genome?
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).

Originally Posted by jwfoley View Post
FYI I tested UniPeak (doi:10.1186/1471-2164-14-720) on the ChIP-exo data from the original paper and it seems to perform nicely with one or two non-default settings. Let me know if you'd like more information.
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.
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