Chromatin Data Analysis

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Chromatin Immunoprecipitation and Assay for Transposase-Accessible Chromatin followed by high-throughput sequencing (ChIp-Seq and ATAC-Seq, respectively) are two popular technologies used to study epigenetic regulations. ChIP-Seq allows the identification of genomic regions bound by a specific protein including histones, while ATAC-Seq evaluates the openness of heterochromatin regions accessible for epigenetic regulation. At Diagenode we have optimized the computing parameters to accurately detect binding sites and accessible chromatin regions. Specific parameters can be customized depending on the specifications of each project.

You can also consult with us for sequencing strategies to determine sequencing depth, read length and pairing mode that will vary greatly depending on the protein of interest and the biological question.

What do we provide with the analysis?

This analysis provides information on each region specifically bound by the targeted protein (peak) as well as its level of enrichment (ChIP-seq) or openness (ATAC-seq).

Standard Analysis

  • Summary statistics (total sequenced reads, total mapping reads, uniquely aligned reads, PCR duplicates, number of peaks, average peak width, reads in peaks, frequency of reads in peaks, etc.)
  • Trimmed and filtered reads in fastQ files after sequencing QC
  • BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)
  • BED files from peak calling (peak location, peak calling score, peak density)
  • Annotation files with location of the peaks within genes

Advanced Analysis

  • Comparative analysis (also called differential analysis) aimed at finding differentially bound sites or uniquely bound sites between two groups of samples
  • Annotation of differentially/uniquely bound sites
  • Determination of specific binding motifs within peaks
  • Gene ontology enrichment analysis on differentially binding/unique sites
  • Pathway enrichment analysis (KEGG or DOSE for human samples)

    Customized Analysis

    If you require a type of analysis that is not in the previous list, please consult with our expert bioinformatics team.




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