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10x Genomics
Chromium Single Cell ATAC

Cell Ranger ATAC count: Peaks File

The peaks.bed file contains the output of the peak calling algorithm. Each peak is an interval on the genome that has a local enrichment of transposase cut-sites. The peaks file reports those intervals in BED format. Cell Ranger ATAC produces peaks that are numerically sorted and non-overlapping. Additionally, header lines beginning with # record information about the sample, the reference used and primary contigs in the reference.

The set of called peaks reflected in this file form the set of primary 'features' that are measured for each cell. Each peak has a corresponding row in the feature-barcode matrix output files.

See the Algorithm Overview page for details on how Cell Ranger ATAC produces peaks.

Column definitions

Column NumberNameDescription
1chromReference genome chromosome of peak
2chromStartStart position of peak on chromosome.
3chromEndEnd position of peak on chromosome. The end position is exclusive, so represents the position immediately following the peak interval.