ATAC Peaks and Peaks Index
Files:
[sample_name]_ATAC_Peaks.bed.gz
[sample_name]_ATAC_Peaks.bed.gz.tbi
The Peaks file is the bgzipped narrowPeak output from MACS2 detecting peak regions of Tn5 transposase activity. The file is a BED6+4 tabular file that has one line for each peak, sorted by chromosome and position. The columns are
| Column | Name | Description |
|---|---|---|
| 1 | chrom | Chromosome or scaffold identifier |
| 2 | chromStart | Zero-indexed start site of peak region |
| 3 | chromEnd | Zero-indexed end site of peak region (non-inclusive) |
| 4 | name | Name of the peak |
| 5 | score | Integer score for display, calculated as int(-10*log10qvalue) |
| 6 | strand | Always a "." because these peak regions are not strand-specific |
| 7 | - | Fold-change at peak summit |
| 8 | - | -log10pvalue at peak summit |
| 9 | - | -log10qvalue at peak summit |
| 10 | - | Summit position relative to peak start |
The Fragments Index is the index file generated by tabix for the coordinate-sorted Peaks file.