https://www.pierre-francois-roux.com/tags/epigenomics/ Recent content in Epigenomics on Pierre-François Roux Hugo -- gohugo.io en-us © 2021 Pierre-François Roux Fri, 19 Jun 2026 09:30:00 +0000 https://www.pierre-francois-roux.com/2026/06/19/atac-seq-is-more-than-a-peak-list/ Fri, 19 Jun 2026 09:30:00 +0000 https://www.pierre-francois-roux.com/2026/06/19/atac-seq-is-more-than-a-peak-list/ Many ATAC-seq analyses stop at peak calling: open regions in condition A, open regions in condition B, differential accessibility. That is useful, but it leaves a lot of information on the table. ATAC-seq libraries carry several layers of signal: chromatin accessibility, fragment architecture, nucleosome positioning, transcription factor footprints, and sometimes even useful genetic information. Look At Fragment Classes The fragment length distribution is one of the first things I inspect. https://www.pierre-francois-roux.com/2026/06/19/a-qc-checklist-before-trusting-chip-seq-or-atac-seq-peaks/ Fri, 19 Jun 2026 09:10:00 +0000 https://www.pierre-francois-roux.com/2026/06/19/a-qc-checklist-before-trusting-chip-seq-or-atac-seq-peaks/ Peak calling is not the beginning of an epigenomic analysis. It is a consequence of many upstream choices: library quality, mapping behavior, duplication, background, blacklisted regions and replicate structure. Before interpreting peaks, I like to ask a simple question: would I trust this experiment if I ignored the peak caller entirely? Start With The Library Check these before any biological interpretation: Per-base quality and adapter content. Fraction of aligned reads. https://www.pierre-francois-roux.com/project/atac-seq-as-an-integrative-assay-for-aging-and-cancer/ Fri, 19 Jun 2026 00:00:00 +0000 https://www.pierre-francois-roux.com/project/atac-seq-as-an-integrative-assay-for-aging-and-cancer/ ATAC-seq is widely used to map chromatin accessibility, but bulk ATAC-seq libraries contain much more information than accessible regulatory elements alone. In recent work, I benchmarked ATAC-seq against matched whole-genome sequencing to evaluate whether a single assay can also recover genetic information relevant to cancer and aging biology. Using paired datasets from patient-derived melanoma cell lines and TCGA brain tumors, we showed that ATAC-seq can support high-precision small variant detection within accessible regions, robust copy-number profiling, mitochondrial genome characterization and telomere-associated repeat quantification, while preserving its classical epigenomic readouts.