Peak Calling Tools 2016-09-09

• SPP
• MACS2
• Cexor (in R) ? Pedro says no.
• Peakranger
• JAMM not now
• GEM
• BayesPeak (in R) (Cairns, Spyrou et al. 2011)
• CCAT (Xu, Handoko et al. 2010)

4 (6) Cell lines or cell types K562 cells (human) and their mouse analog, MEL H1-hESC embryonic stem cells (human), and E14 ES (mouse) Possibly, GM12878 lymphoblastoid cells (human), and their mouse analog, CH12.LX

7 Transcription factors FOXA GABP MYC MAX KAT2A NRSF STAT

5 Histone modifications

H3K36me3 H3K4me3 H3K27ac H3K27me3 H3K4me1

hg19: 34 experiments total

mm9: 3 cell types: CH12.LX, ES-E14, MEL