ChIP-Seq Data Analysis: GWAS SNP Enrichment and Peak Association Insights
Explore the ChIP-Seq analysis pipeline, GWAS SNP enrichment, and the association between ChIP-Seq peaks and GWAS SNPs in different diseases. Discover the significance of H3K27ac peaks, disorder SNPs, and more in this comprehensive study.
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GWAS SNP enrichment on ChIP-Seq data SL- P2-tech
ChIP-Seq analysis pipeline Quality metrics of read counts (Strand cross- correlation analysis, number of reads in the peaks, library complexity) Signal generation, file format conversion (samtools, bedtools, bedGraphToBigWig) Read mapping (Bowtie) Quality metrics (FastQC, FASTX) ChIP FastQ file ChIP bigwig file Signal generation, file format conversion (samtools, bedtools, bedGraphToBigWig) Read mapping (Bowtie) Quality metrics (FastQC, FASTX) Control FastQ file Check peak calling results Control bigwig file Peak calling (MACS2, MUSIC) ChIP-Seq peaks Downstream analysis (peak comparison, peak annotation, motif analysis) 2
Association of ChIP-Seq peaks and GWAS SNPs of different diseases H3K27ac peak Disorder SNPs Common 1000 genome SNPs Mapped positionn Row total Maped to ChIP peaks a b a+b Not mapped to ChIP peaks c d c+d Column total a+c b+d N=a+b+c+d Enrichment = -log10(p value by one-tailed Fisher s exact test) http://www.rasadbsnp.com/images/SNPs.jpg 3
GWAS SNPs enrichment in ChIP-Seq peaks Brainspan Roadmap 4
ChIP-Seq analysis pipeline Quality metrics of read counts (Strand cross- correlation analysis, number of reads in the peaks, library complexity) Quality metrics (FastQC, FASTX) Signal generation, file format conversion (samtools, bedtools, bedGraphToBigWig) ChIP FastQ file Read mapping (Bowtie) ChIP bigwig file Quality metrics (FastQC, FASTX) Signal generation, file format conversion (samtools, bedtools, bedGraphToBigWig) Read mapping (Bowtie) Control FastQ file Control bigwig file Check peak calling results Peak calling (MACS2, MUSIC) ChIP-Seq peaks ROSE: Rank ordering of super-enhancers Super-enhancers 5
