Question: When running cellranger-atac count I encountered the following: [error] Entry 0 in sample_defs are missing input FASTQs. What is the cause and solution?
Answer: The pipeline couldn't start because the FASTQ directory is missing the R3 file. For cellranger-atac count, the I1 FASTQ is optional but the R1, R2, and R3 FASTQ files are all mandatory for the analysis.
| RunInfo.xml | FASTQ name | Purpose | Length |
| Read Number = "1" | R1 | Transposed DNA | 50 |
| Read Number = "2" | I1 | Sample index (i7) | 8 |
| Read Number = "3" | R2 | 10x barcode (i5) | 16 |
| Read Number = "4" | R3 | Transposed DNA | 50 |
This error typically occurs when the BCL files are demultiplexed with cellranger mkfastq (which is designed for single cell gene expression data) instead of cellranger-atac mkfastq (which is used for single cell ATAC data). The solution is to re-demultiplex with the proper pipeline here: Single Cell ATAC Software Downloads.
Products: Single Cell ATAC