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.
|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