Cell Ranger ARC1.0, printed on 11/05/2024
The cellranger-arc pipeline outputs a position-sorted and indexed BAM file of read alignments to the genome and transcriptome. Reads aligned to the transcriptome across exon junctions in the genome tend to have a large gap in their CIGAR string i.e. 35M225N64M. Each read in this BAM file has a 10x Chromium cellular (associated with a 10x gel bead) barcode and molecular barcode information attached. Cell Ranger ARC modifies MAPQ values; see the MM tag below. The following assumes basic familiarity with the BAM format. More details on the the SAM/BAM standard are available online.
10x Chromium barcode (associated with a 10x gel bead) 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. |
UB |
Z | Chromium molecular barcode sequence that is error-corrected among other molecular barcodes with the same cellular barcode and gene alignment. |
UR |
Z | Chromium molecular barcode sequence as reported by the sequencer. |
UY |
Z | Chromium molecular barcode read quality. Phred scores as reported by sequencer. |
The cell barcode CB
tag includes a suffix with a dash separator
followed by a number:
AGAATGGTCTGCAT-1
This number denotes what we call a GEM well, and is used to serialize barcodes in order to achieve a higher effective barcode diversity when combining samples generated from separate GEM chip channel runs. Note that Cell Ranger ARC does not support multi-GEM-well analysis at this time. Normally, this number will be "1" across all barcodes when analyzing a sample generated from a single GEM chip channel. 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.
The following tags will also be present on reads that mapped to the genome and
overlapped either an exon or an intron by at least one base pair (default mode).
When cellranger-arc count is run with the
--gex-exclude-introns
argument, alignment tags are restricted to
reads overlapping exons. A read may align to multiple transcripts and genes, but
it is only considered confidently mapped to the transcriptome if it maps to a
single gene.