10x Genomics
Chromium Single Cell CNV
Cell Ranger DNA1.1, printed on 11/21/2024
Cell Ranger DNA Algorithms Overview
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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.
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The algorithms in the cellranger-dna cnv pipeline take as input
- Paired-end sequencing reads from a Chromium Single cell CNV library
- A reference genome
and produces as output
- Copy number calls for each cell
- A hierarchical clustering of cells based on mutual similarity
- Copy number calls for each group of cells defined by the hierarchical clustering
The algorithms can be organized into:
- Preprocessing
- Strip the 10x barcode from each read pair
- Align the reads to the reference genome
- Identify barcodes that correspond to cells
- Compute a coverage profile matrix for each cell at 20 kilobase (kb) genome resolution
- Determine the mappable regions of the genome by simulation
- Single cell copy number calling
- Estimate the copy number for each cell over the mappable regions of the genome
- Impute copy number values over the non-mappable regions
- Clustering
- Build a hierarchical clustering of cells using the single cell copy number calls
- Construct a read coverage profile matrix for each group of cells defined by the hierarchical clustering
- Determine the copy number for each group of cells defined above
