Cell Ranger DNA1.1, printed on 12/26/2024
| Analysis software for the 10x Genomics single cell DNA product is no longer supported. Raw data processing pipelines and visualization tools are available for download and can be used for analyzing legacy data from 10x Genomics kits in accordance with our end user licensing agreement without support. |
The cellranger-dna cnv 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. |
The following assumes basic familiarity with the BAM format. More details on the SAM/BAM standard are available online.
Chromium cellular and molecular barcode information for each read is stored as TAG fields:
| Tag | Type | Description |
|---|---|---|
CB | Z | Chromium cellular barcode sequence that is error-corrected and confirmed against a list of known-good barcode sequences. |
CR | Z | Chromium cellular barcode sequence as reported by the sequencer. |
CY | Z | Chromium cellular barcode read quality. Phred scores as reported by sequencer. |
BC | Z | Sample index read. |
QT | Z | Sample index read quality. Phred scores as reported by sequencer. |
GP | Z | 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. |
MP | Z | 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 suffix "-1" that labels the GEMs from a single channel and we call a GEM group.
AGAATGGTCTGCAT-1
Cell Ranger DNA currently only supports libraries generated from a single GEM run and so the 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.