Recommendation list

Bowtie(PE)-MACS2-GADEM-MotIV-ChIPpeakAnno
Bowtie(SE)-MACS2-GADEM-MotIV-ChIPpeakAnno
Bowtie(SE)-ZINBA-GADEM-MotIV-ChIPpeakAnno
Bowtie(SE)-SICER-GADEM-MotIV-ChIPpeakAnno

Related list

MACS2 with control(input) (2.0.10 and later)
PeakSeq
SISSRs
ChIPpeakAnno add neighbor annotation and make a report
SISSRs (SE)
DEGseq:FET for SISSRs
FastQC (SE)
Bowtie (SE) + GE

Note "SE": For single-end read, "PE": For paired-end read, "GE": Genome explorer which is our original genome browser.
It is necessary to register to analyze your own data.
: The popular pipeline or the latest one that the developer recommend.
Notice: Unrecomend not a tool used by the pipeline but the workflow of the pipelie.

References:

• BMC Genomics. 2009; 10: 618.
• Waki et al. PLoS Genetics, 2011
• Genome Biology 2010, 11:R69