ChIP-Seq data for H3K4me2, H3K9me2, and H3K27me3 were analyzed using PePr
in order to identify regions in the D. melanogaster genome that are enriched for these histone
Reads from the two replicates for each histone modification were provided to PePr in a single run.
Regions enriched in H3K4me2 were identified using PePr with the following parameters:
Regions enriched in H3K9me2 and H3K27me3 were identified using PePr with the following parameters:
Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA.
PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data.
Bioinformatics. 2014 Sep 15;30(18):2568-75.