Genomic intervals & annotation / Peak annotation
Your data stays in your browser: files are read and processed on your device, never uploaded to any server, and cleared when you close the page. Free, no sign-in.
Each peak is placed in one class by priority: promoter (within the chosen distance upstream or downstream of any transcript TSS) > exon > intron (inside a gene but not in an exon) > intergenic. Peaks are assigned by their centre by default, or by any overlap.
The nearest gene is the one whose TSS (start for +, end for − strand) is closest to the peak centre; distances follow the gene direction, so negative values mean the peak is upstream of the TSS. “overlapping_genes” lists genes overlapping the assigned region.
The pie chart shows the share of each class; the bar chart shows distances to the nearest TSS. Peaks of transcription factors or active histone marks usually cluster near TSSs; a high intergenic share may point to distal regulatory elements.
Genes without exon annotation (bacterial annotations often carry only CDS) use their CDS, or the whole gene, as exons. Chromosome names must match between peaks and annotation.
Region assignment by priority and distance to the nearest TSS follow the approach of Yu et al. 2015 (Bioinformatics 31:2382) and Heinz et al. 2010 (Mol Cell 38:576); results were checked line by line against an independent Python reference implementation.
Runs in your browser; up to roughly 500,000 peaks and annotation files up to about 100 MB are recommended.
Send us your data and research question and you will receive a written plan within 1 working day: analysis steps, parameter rationale, deliverables and timeline. Quoted per project.