The cellranger
pipeline outputs an indexed BAM file containing position-sorted reads aligned to the genome and transcriptome, as well as unaligned reads. If Feature Barcode libraries are present in the analysis, the BAM file will also contain aligned and unaligned records for each library type (e.g., Antibody Capture, CRISPR Guide Capture, 3' Cell Multiplexing, Antigen Capture).
BAM files can be used for troubleshooting reads that were unaligned or for converting BAM files back to FASTQ files. Each read in this BAM file has Chromium cellular and molecular barcode information attached. The following tables assume basic familiarity with the BAM format. The Type column refers to the type of value stored in the tag (see the SAM/BAM standard) documentation for details.
Some aspects of the BAM file are particular to Fixed RNA Profiling samples. The mapping quality (MAPQ) values described here do not apply to 3' or 5' Gene Expression data.
A read that multi-maps to the reference transcriptome, but maps uniquely to a single probe, is considered confidently mapped to that probe and its gene. The mapping quality has the following definition:
MAPQ | Description |
---|---|
255 | Both read halves map to the same probe. |
3 | Each read half maps to a different probe. |
1 | One read half maps to a probe and the other half does not |
0 | Neither read half maps to a probe |
This Analysis Guide tutorial walks users through the process of identifying records in the BAM file that contribute to UMI counting: Navigating 10x Genomics Barcoded BAM Files. Note: 10x Genomics does not provide support for community-developed tools and makes no guarantees regarding their function or performance. Please contact tool developers with any questions. If you have feedback about Analysis Guides, please email [email protected].