ATAC Transposase Sites and Index file
Files:
[sample_name]_ATAC_Transposase_Sites.bed.gz
[sample_name]_ATAC_Transposase_Sites.bed.gz.tbi
The Transposase Sites file is a BED3+2 tabular file that has one line per transposase cut site (represented by a base at each end of 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 barcode, 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 location of transposase site |
| 3 | chromEnd | chromStart + 1 |
| 4 | cellIndex | BD Rhapsody™ bead index (integer) |
| 5 | readSupport | Count of read-pairs that support the existence of the associated fragment |
The Transposase Sites Index is the index file generated by tabix for the coordinate-sorted Transposase Sites file.