Cell Ranger ATAC2.1, printed on 03/04/2024
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).
|Barcode-corrected reads aligned to the user-specified reference, sorted by reference position.
|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.
Chromium cellular barcode and mapping information for each read is stored as TAG fields:
|Chromium cellular barcode sequence that is error-corrected and confirmed against a list of known-good barcode sequences.
|Chromium cellular barcode sequence as reported by the sequencer.
|Chromium cellular barcode read quality. Phred scores as reported by sequencer.
|Sample index read.
|Sample index read quality. Phred scores as reported by sequencer.
|Adapter sequence trimmed off the end of the read.
|Base 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.