Epigenomic analysis of chromatin and methylation
From FASTQ to result: peak calling for ATAC-seq and ChIP-seq (MACS3) and DNA methylation profiling by WGBS (Bismark), with quality control and an interpretable summary.
Two families, one reproducible workflow
We analyze the epigenomic sequencing data you already have, with versioned pipelines and per-sample quality control.
ATAC-seq — accessibility
Alignment, quality control (fragment sizes, enrichment at TSS) and peak calling of open chromatin.
MACS3 · QCChIP-seq — factors and marks
Peak calling with optional control; narrow mode for transcription factors and broad for broad histone marks.
narrow / broadWGBS — DNA methylation
Bisulfite alignment with Bismark, per-cytosine methylation extraction and global (CpG) profile per sample.
Bismark · %mCPeak summary
Number of peaks, coordinates, q-value and summit per region; a table ready for downstream analysis.
narrowPeak / broadPeakMethylation summary
Global methylation (%mC), mean %mC per CpG and number of CpGs covered; the basis for comparing conditions.
global %mCNext steps
On peaks: annotation to genes, motifs and differential regions. On methylation: differentially methylated regions (DMRs) and annotation.
On requestFrom read to result
1. Data
FASTQ (or BAM) + genome reference; for ChIP, the control if available.
2. Alignment
Mapping and per-sample quality control.
3. Analysis
Peak calling (MACS3) or methylation extraction (Bismark).
4. Result
Peaks (narrowPeak/broadPeak) or methylation profile + summary.
What it includes
Alignment, quality control, peak calling (ATAC/ChIP) or methylation profile (WGBS), results tables and an interpretable summary. Annotations and DMRs as an extension. Volume and academic discounts.
Honest limits
With little data or single-end sequencing, peak calling requires adjustments (nomodel/extsize) that we document. Differentially methylated regions (DMRs) are an additional step. We deliver everything as research (RUO).
Other research services
Shall we analyze your epigenomics?
Tell us the assay (ATAC/ChIP/WGBS), number of samples and reference; we get back to you with a quote and timeline within 48 h.