Cell Ranger ARC requires Illumina gene expression (GEX) and ATAC FASTQ files as input, which typically come from running demultiplexing software (e.g., Illumina's BCL Convert). However, it is possible to use FASTQ files from other sources, such as a published dataset or the 10x Genomics bamtofastq tool.

To serve as inputs for Cell Ranger ARC, GEX and ATAC FASTQ files should conform to the naming conventions shown below.

[Sample Name]_S1_L00[Lane Number]_[Read Type]_001.fastq.gz

or

[Sample Name]_S1_[Read Type]_001.fastq.gz

Where Read Type is one of:

• I1: Dual index i7 read (optional)
• I2: Dual index i5 read (optional)
• R1: Read 1
• R2: Read 2

[Sample Name]_S1_L00[Lane Number]_[Read Type]_001.fastq.gz

Where Read Type is one of:

• I1: Dual index i7 read (optional)
• R1: Read 1
• R2: Dual index i5 read
• R3: Read 2

Cell Ranger ARC will also accept ATAC FASTQs in this format:

• I1: Dual index i7 read (optional)
• R1: Read 1
• I2: Dual index i5 read
• R2: Read 2

The cellranger-arc count pipeline can process data from one Multiome ATAC library and one Multiome GEX library, each of which could be sequenced on multiple flow cells. Multi-library analysis is not possible at this time. cellranger-arc count cannot be used to process GEX or ATAC data alone.

The FASTQ files are specified using a libraries CSV file and passed to the cellranger-arc count pipeline using the --libraries argument.

Cell Ranger ARC scans the folder's subdirectories to locate the *.fastq.gz files. Make sure there are no duplicate sequence files in the subdirectories.