Closed yejg2017 closed 10 months ago
Hey yejg2017-- any luck with this? I'm having a similar problem.
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.
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!