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# Cell Ranger ATAC count: Fragments File

The cellranger-atac 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.

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.

## Fragment interval

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 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.

## Format

The pipeline outs/ folder contains fragments.tsv.gz and fragments.tsv.gz.tbi. The fragments.tsv.gz contains one line per unique fragment, with tab-separated fields as described below. Additionally, header lines beginning with # record information about the sample, the reference used and primary contigs in the reference. The data is block-gzipped to allow indexing and to save disk space. The 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 fragments.tsv.gz file, as in a BED file, are 0-based.

## Column definitions

Column NumberNameDescription
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.
5 readSupport The total number of read pairs associated with this fragment. This includes the read pair marked unique and all duplicate read pairs.