HOME  ›   pipelines
If your question is not answered here, please email us at:  ${email.software}

10x Genomics
Chromium Single Cell ATAC

Cell Ranger ATAC count: Barcoded BAMs

The cellranger-atac count pipeline outputs a single position-sorted and indexed BAM file. These files are primarily provided for use with a BAM visualization tool such as the Integrated Genome Viewer (IGV).

File Records Reference Description
possorted_bam.bam Reads User-specified reference Barcode-corrected reads aligned to the user-specified reference, sorted by reference position.
possorted_bam.bam.bai Index User-specified reference Index file enabling random access to BAM by position

The following assumes basic familiarity with the BAM format. More details on the SAM/BAM standard are available online.

BAM Barcode Tags

Chromium cellular barcode and mapping information for each read is stored as TAG fields:

CBZChromium cellular barcode sequence that is error-corrected and confirmed against a list of known-good barcode sequences.
CRZChromium cellular barcode sequence as reported by the sequencer.
CYZChromium cellular barcode read quality. Phred scores as reported by sequencer.
BCZSample index read.
QTZSample index read quality. Phred scores as reported by sequencer.
TRZAdapter sequence trimmed off the end of the read.
TQZBase quality for the trimmed adapater sequence. Phred scores as reported by sequencer.

The cell barcode CB tag includes a gem group suffix "-1" that labels the GEMs from a single channel.


cellranger-atac count only supports libraries generated from a single GEM run and so the gem group suffix is always -1. It can either be left in place and treated as part of a unique barcode identifier, or explicitly parsed out to leave only the barcode sequence itself.