ATAC Fragments and Fragments Index
Files:
[sample_name]_ATAC_Fragments.bed.gz
[sample_name]_ATAC_Fragments.bed.gz.tbi
The Fragments file is a BED3+2 tabular file that has one line for each fragment, sorted by chromosome and position. The first three columns are the same that all BED files use, making this file function as a BED file for many purposes, while the last two diverge from the BED specification. The fourth column is the fragment's cell index, identifying the specific BD Rhapsody™ bead that bound the fragment. The fifth column shows the total number of aligned read-pairs associated with the fragment, including any duplicates.
| Column | Name | Description |
|---|---|---|
| 1 | chrom | Chromosome or scaffold identifier |
| 2 | chromStart | Zero-indexed Tn5-adjusted start site of fragment |
| 3 | chromEnd | Zero-indexed Tn5-adjusted end site of fragment (non-inclusive) |
| 4 | cellIndex | BD Rhapsody™ bead index (integer) |
| 5 | readSupport | Count of read-pairs that support the existence of this fragment |
The Fragments Index is the index file generated by tabix for the coordinate-sorted fragments file.