Cell Ranger ATAC2.0, printed on 12/26/2024
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][1] 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][3].
See the [Algorithm Overview][2] 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. |
[1]: https://genome.ucsc.edu/FAQ/FAQformat.html#format1 "BED Format" [2]: ../algorithms/overview "Algorithm Overview" [3]: matrices "Matrix Output Files"