Cell Ranger ARC1.0, printed on 12/22/2024
The Cell Ranger ARC count pipeline outputs a BED-like tabular file, where each line represents a unique ATAC-seq fragment captured by the assay. Each fragment is created by two separate transposition events, which create the two ends of the observed fragment. Each unique fragment may generate multiple duplicate reads. These duplicate reads are collapsed into a single fragment record. There is a record in the fragment file for every non-chimeric read pair alignment with mapping quality > 30 where both reads map to a nuclear contig containing at least one gene.
The first three columns of the fragments file are defined as in the BED format, so the fragments file can be treated as BED file in many cases.
The BED interval of the fragment is obtained by adjusting the BAM alignment interval of the sequenced read-pair. The start of the interval is moved forward by 4 bp from a left-most alignment position and backward by 5 bp from the right-most alignment position. The transposase cuts the two DNA strands with a 9 bp overhang, and adjusted positions represent the center point between these cuts; this position is recorded as a cut site that represents a chromatin accessibility event.
The pipeline outs/ folder contains atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi. The atac_fragments.tsv.gz contains one line per unique fragment, with tab-separated fields as described below. The data is block-gzipped to allow indexing and to save disk space. The atac_fragments.tsv.gz.tbi file is a tabix index of the fragment intervals facilitating random access to records from an arbitrary genomic interval. The tabix index is created with --preset=bed.
Positions in the atac_fragments.tsv.gz file, as in a BED file, are 0-based.
| Column Number | Name | Description |
|---|---|---|
| 1 | chrom | Reference genome chromosome of fragment |
| 2 | chromStart | Adjusted start position of fragment on chromosome. |
| 3 | chromEnd | Adjusted end position of fragment on chromosome. The end position is exclusive, so represents the position immediately following the fragment interval. |
| 4 | barcode | The 10x cell barcode of this fragment. This corresponds to the CB tag attached to the corresponding BAM file records for this fragment. Note: this is an in silico translated barcode sequence that matches the Gene Expression barcode sequence on the same gel bead. See Barcode Translation for more details. |
| 5 | duplicateCount | The number of PCR duplicate read pairs observed for this fragment. Sequencer-created duplicates, such as Exclusion Amp duplicates created by the NovaSeq™ instrument are excluded from this count. |