Cell Ranger ATAC1.2, printed on 12/22/2024
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.
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 Number | Name | Description |
|---|---|---|
| 1 | chrom | Reference genome chromosome of peak |
| 2 | chromStart | Start position of peak on chromosome. |
| 3 | chromEnd | End position of peak on chromosome. The end position is exclusive, so represents the position immediately following the peak interval. |