Workflow and Tools for Integrating ChIP-seq and RNA-seq Data Analysis

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Tags: software, processing, tool

Here is a concise summary of the key steps and tools for ChIP-seq and RNA-seq data analysis and integration:

  1. Quality control: FastQC for assessing raw sequencing data quality.

  2. Trimming and filtering: Trimmomatic or Cutadapt for preprocessing reads.

  3. Alignment: Bowtie2 or BWA for ChIP-seq, and STAR, HISAT2, or TopHat2 for RNA-seq.

  4. Peak calling (ChIP-seq): MACS2, SICER, HOMER (see separate article) or diffReps.pl (part of the DiffReps package) for identifying bound genomic regions.

  5. Gene expression quantification (RNA-seq): featureCounts, HTSeq, or Cufflinks for expression levels.

  6. Differential expression analysis (RNA-seq): DESeq2 or edgeR for comparing conditions or time points.

  7. Motif analysis (ChIP-seq): MEME-ChIP for identifying enriched sequence motifs.

  8. Data visualization: deepTools or Integrative Genomics Viewer (IGV) for viewing aligned reads and peaks.

  9. Annotation and integration: ChIPseeker or HOMER for peak annotation, and GenomicRanges, DiffBind, or other R packages for integrating ChIP-seq and RNA-seq data.

  10. Functional enrichment analysis: GSEA, clusterProfiler, or DAVID for pathway and functional category enrichment.

  11. Visualization: ggplot2 or ComplexHeatmap for combined ChIP-seq and RNA-seq data.

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