10x Genomics
Chromium Single Cell CNV

Cell Ranger DNA1.1, printed on 11/20/2024

What is Cell Ranger DNA?

Cell Ranger DNA is a set of analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation (CNV), and compare heterogeneity among cells.

Pipelines

Cell Ranger DNA includes five main pipelines:

• cellranger-dna mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files.

• cellranger-dna cnv takes FASTQ files from cellranger-dna mkfastq and performs reference alignment, cell calling, copy number estimation and hierarchical clustering.

• cellranger-dna bamslice takes a BAM file from cellranger-dna cnv and subsets it to specified cells of interest.

• cellranger-dna aggr aggregates outputs from multiple runs of cellranger-dna cnv, aggr, or reanalyze); and reperforms secondary analysis including copy number estimation and hierarchical clustering.

• cellranger-dna reanalyze takes the HDF5 output of an existing cellranger-dna cnv, aggr, or reanalyze run, restricted to the selected barcodes or group of interest, and reperforms copy number estimation and hierarchical clustering.

Output is delivered in standard HTML, CSV, BED, BAM and HDF5 formats.

Terminology

Throughout the documentation, you will see references to samples, libraries, sequencing runs, Martian and pipestance. We define these as follows:

• Sample: A cell suspension extracted from a single biological source (blood, tissue, etc).
• Library: A 10x-barcoded sequencing library prepared from a single sample, corresponding to a single chip channel of a 10x Chromium Controller run.
• Sequencing Run or Flowcell: A flowcell containing data from one sequencing instrument run. The sequencing data can be further addressed by lane and by one or more sample indices.
• Martian: An open-source language and framework for running computational pipelines. Cell Ranger DNA pipelines utilize this framework. For more information see the Martian website.
• Pipestance or Pipeline instance: A Cell Ranger DNA pipestance refers to the folder that contains all the data produced by a single Martian pipeline invocation. For more details refer to the Pipestance structure page.

Note that a single library may be sequenced across multiple flowcells, and then combined as if all the reads came from one sequencing run. Additionally, a single flowcell may contain multiple libraries, separated using different lanes and / or sample indices.

Cell Ranger DNA allows for the analysis of a single 10x-barcoded sequencing library prepared from a sample that is sequenced across one or more flowcells. The analysis of multiple libraries generated from the same sample, for example using multiple channels on a chip, is not currently supported.