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10x Genomics
Chromium Single Cell Multiome ATAC + Gene Exp.

Peaks file

The atac_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 ARC produces peaks whose coordinates are numerically sorted and non-overlapping and whose chromosomes are sorted in the same order as the reference genome.

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 ARC produces peaks.

Note: cellranger-arc count can be run with a user-specified BED file containing peaks using the --peaks argument as described here

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.