Cell Ranger ATAC1.1, printed on 06/06/2023
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).
|possorted_bam.bam||Reads||User-specified reference||Barcode-corrected reads aligned to the user-specified reference, sorted by reference 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:
|Z||Chromium cellular barcode sequence that is error-corrected and confirmed against a list of known-good barcode sequences.|
|Z||Chromium cellular barcode sequence as reported by the sequencer.|
|Z||Chromium cellular barcode read quality. Phred scores as reported by sequencer.|
|Z||Sample index read.|
|Z||Sample index read quality. Phred scores as reported by sequencer.|
|Z||Adapter sequence trimmed off the end of the read.|
|Z||Base quality for the trimmed adapater sequence. Phred scores as reported by sequencer.|
|i||Genome position. Note: this is an auxiliary tag used for the purpose of duplicate marking and is not intended for downstream use. We intend to deprecate this tag in subsequent versions.|
|i||Genome position of mate-pair. Note: this is an auxiliary tag used for the purpose of duplicate marking and is not intended for downstream use. We intend to deprecate this tag in subsequent versions.|
The cell barcode
CB tag includes a gem group suffix "-1" that labels the GEMs from a single channel.
Cell Ranger ATAC currently 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.