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
- 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)
