ChIP-seq #
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A method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with NGS to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest. (http://en.wikipedia.org/wiki/ChIP-sequencing)

(Image from ChIP–seq: advantages and challenges of a maturing technology 2009-10-10, Nature Review Genetics)

(Image from First Analysis of Tumor-Suppressor Interactions with Whole Genome in Normal Human Cells Reveals Key Differences with Cancer Cells 2011-11-30 )

The result is usally according to target protein (by antigen)

FASTQ
BAM
WIG (bigWig)
BED
- broadPeak: called regions of signal enriched based on pooled, normalized data
- narrowPeak: called peaks of signal enriched based on pooled, normalized data
YLF (ELAND)

And it can be incoporated to UCSC Genome Browser.

데이터 분석 방법
1. General workflow
2. 유전자 어노테이션
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데이터 분석 방법 #

General workflow #

Start from FASTQ files
QC by FastQC
Trim, crop, remove adapters by Trimmomatic
Alignment by Bowtie
Peak calling by MACS
Peak annotation by ChIPseeker
Motif analysis by HOMER
Heatmap by ngs.plot

유전자 어노테이션 #

UCSC Table Browser에서 전체 gene 정보를 BED 파일로 받는다. 이때 Upstream 2.5k를 선택하면, TSS 앞 2.5k 영역의 위치를 받는다.
스크립트로 TSS 뒤 2.5k를 늘려준다. (strand 정보 참고하여, 앞 혹은 뒤) - hg19-tss-5k.bed 파일 저장
MACS 프로그램 결과인 bigwig 파일을 bigWigToWig 명령으로 WIG 변환
BEDOPS의 wig2bed 프로그램으로 BED 변환 후, bedmap 프로그램으로 매핑 (참고)

$ wig2bed < in.wig | bedmap --echo --echo-map-score genes.bed - > answer.bed
answer.bed에 있는 refseq id로 유전자 확인