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Cellranger multiome atac gex

CellRanger Multiome ATAC + GEX

Data Type

Analyze Single Cell Multiome ATAC + Gene Expression data using the CellRanger ARC software suite provided by 10X Genomics.

Input Data:

After processing a sample for Multiome ATAC + Gene Expression, raw sequencing data will be produced in the form of FASTQ files both for chromatin accessibility (ATAC) as well as gene expression (GEX) information. In order to analyze these datasets, the FASTQ files must be marked appropriately according to the data type that they represent.

The best way to annotate the input FASTQ data is using a samplesheet.csv with columns for:

  • sample: Identifier for the sequencing library
  • fastq_1: Name of the R1 (or I1) FASTQ file
  • fastq_2: Name of the R2 (or I2) FASTQ file
  • grouping: Identifier for the sample analyzed for both GEX and ATAC
  • feature_types: Either Gene Expression, or Chromatin Accessibility

Example:

sample,fastq_1,fastq_2,grouping,feature_types
sampleA_gex,sampleA_gex_S1_L001_R1_001.fastq.gz,sampleA_gex_S1_L001_R2_001.fastq.gz,sampleA,Gene Expression
sampleA_atac,sampleA_atac_S2_L001_R1_001.fastq.gz,sampleA_atac_S2_L001_R2_001.fastq.gz,sampleA,Chromatin Accessibility

Note: The file described above should be named samplesheet.csv and can be uploaded either (1) along with the FASTQ files during initial upload or (2) by clicking on the "Upload Samplesheet" button for a previously-uploaded dataset.

Parameters:

  • Reference Genome: Select the appropriate reference genome (human or mouse)
  • CellRanger ARC Version: Specify the CellRanger ARC software version to be used for analysis
Technical Details

Workflow Repository: github.com/FredHutch/nf-cellranger-tools

Citations:

This pipeline supports viewing its output using the embedded Single-Cell Dashboard App directly on the output dataset's Overview page.