ChIP-seq基本流程及工具

ChIP-seq数据分析整理

• 1.Alignment
• 2.Peak detection
• 3.Peak annotation
• 1. GO analysis
• 2. Pathway analysis
• 4.Differential analysis
• 5.Peak gene
• 6.Pathway analysis
• 7.Data visualization

1.Alignment

base calling——Off-Line Basecaller software (OLB V1.8.0).

Solexa CHASTITY quality filter【质量控制】

http://www.genomics.agilent.com/article.jsp?pageId=2213

BOWTIE software (V2.1.0)

2.Peak detection

MACS v1.4

p-value 10^-5

3.Peak annotation

UCSC RefSeq

Peaks annotation

• TSS distribution heatmap
• Peak Distribution around TSS
• peak Distribution Pie Charts

Peaks in promoter

1. GO analysis

www.geneontology.org

• Biological Process（BP）
• Cellular Component(CC)
• Molecular Function(MF)

7files

GO Biological Process Classification Enrichment Score Fold Enrichment P-value Tree Result.txt Result.html Result.xls

GO Cellular Component Classification GO Molecular Function Classification

2. Pathway analysis

KEGG

4.Differential analysis

RefSeq

diffReqs

5.Peak gene

GREAT

6.Pathway analysis

KEGG

7.Data visualization

View big file or

WordPad

Fax Viewer

UCSC Genome Browser (wig)