Fastq format???

[yejg2017]

When I run cellrange-arac count,and the fastqs' format in fastq path /Data/PCV-6 is : PCV-6_S1_L001_I1_001.fastq.gz PCV-6_S1_L001_I1_002.fastq.gz PCV-6_S1_L001_I1_003.fastq.gz PCV-6_S1_L001_I1_004.fastq.gz PCV-6_S1_L001_I2_001.fastq.gz PCV-6_S1_L001_I2_002.fastq.gz PCV-6_S1_L001_I2_003.fastq.gz PCV-6_S1_L001_I2_004.fastq.gz PCV-6_S1_L001_R1_001.fastq.gz PCV-6_S1_L001_R1_002.fastq.gz PCV-6_S1_L001_R1_003.fastq.gz PCV-6_S1_L001_R1_004.fastq.gz PCV-6_S1_L001_R2_001.fastq.gz PCV-6_S1_L001_R2_002.fastq.gz PCV-6_S1_L001_R2_003.fastq.gz PCV-6_S1_L001_R2_004.fastq.gz

Data and I run the code ： cellranger-atac count --id=PCV --fastqs=/Data/PCV-6 --reference=refdata-cellranger-atac-GRCh38-1.2.0 --sample=PCV-6

But I always get the error: [error] Entry 0 in sample_defs are missing input FASTQs. I can not find the problem and how to fix it.Counld you help ye ,thanks!

[tdfy]

Hey yejg2017-- any luck with this? I'm having a similar problem.

[alirizaaribas-ibg]

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.

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](https://support.10xgenomics.com/single-cell-atac/software/downloads/latest). https://kb.10xgenomics.com/hc/en-us/articles/360041540451--error-Entry-0-in-sample-defs-are-missing-input-FASTQs Is it correct solution?