# ChIP-seq, CUT&RUN, CUT&Tag and ATAC-seq analysis
URL: https://omicsquest.com/services/chip-seq-cut-and-run-atac-seq-analysis/

OmicsQuest analyzes bulk chromatin data: ChIP-seq (TF and histone), CUT&RUN, CUT&Tag, ATAC-seq, DNase-seq and DNA methylation (WGBS, EM-seq, RRBS, arrays). We follow ENCODE-style QC, call peaks with the right model for narrow or broad marks, use spike-in normalization where appropriate, test differential binding with DiffBind or csaw, and integrate with RNA-seq to connect chromatin changes with expression. Pricing starts at $79/hour.

## Analyses
### QC and peak calling
- **ENCODE-style QC**: FRiP, NSC/RSC, library complexity, IDR for replicate concordance.
- **Peak calling**: MACS2/3 narrow and broad modes, SEACR for CUT&RUN/CUT&Tag.
- **Spike-in normalization**: Drosophila or E. coli spike-in scaling for global changes (e.g., EZH2 or BET inhibition).
- **Blacklist and artifact filtering**: ENCODE blacklist and high-signal region removal.
### Differential and functional analysis
- **Differential binding/accessibility**: DiffBind, csaw and DESeq2 on consensus peaks.
- **Motif analysis**: HOMER and MEME-ChIP de novo and known motif enrichment.
- **Super-enhancer calling**: ROSE on H3K27ac.
- **Chromatin state segmentation**: ChromHMM across multiple marks.
- **Peak annotation and GREAT**: Genomic distribution and regulatory domain enrichment.
### DNA methylation
- **Bisulfite and EM-seq processing**: Bismark, methylation calling and coverage QC.
- **Differentially methylated regions**: DSS, dmrseq and methylKit.
- **Array analysis**: minfi/SeSAMe processing of EPIC and 450K arrays, epigenetic clocks.
### Integration
- **Integration with RNA-seq**: Link differential peaks to differentially expressed genes.
- **Hi-C and 3D context**: Overlay with chromatin loops and TADs where available.

## Deliverables
- QC report with IDR and FRiP
- Peak sets and normalized bigWig tracks
- Differential binding tables
- Motif results and browser figures
- Methods and code

## Mistakes we avoid
- **Missing input or IgG control**: Without controls, open chromatin and sticky regions look like binding. We require or substitute appropriate controls and flag limits.
- **Ignoring global changes**: If a treatment changes total histone marks, standard normalization hides it. We use spike-ins when the biology calls for it.
- **Narrow-peak calling on broad marks**: H3K27me3 and H3K36me3 need broad-domain methods.

## FAQ
**CUT&RUN or ChIP-seq: does the analysis differ?**
Yes. CUT&RUN and CUT&Tag have low background and often need SEACR or adjusted MACS settings, different duplicate handling and, where needed, E. coli carry-over or spike-in normalization.

**Can you integrate ChIP-seq with RNA-seq?**
Yes. We link binding or accessibility changes to target genes and test whether chromatin changes explain expression changes.

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Source: https://omicsquest.com/services/chip-seq-cut-and-run-atac-seq-analysis/ | OmicsQuest, contact@omicsquest.com