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I am grateful for your assistance. I am a novice in using cellranger. While executing cellranger count, I encountered an error. Below is the error message.
ERROR: No input FASTQs were found for the requested parameters.
If your files came from bcl2fastq or mkfastq:
Make sure you are specifying the correct --sample(s), i.e. matching the sample sheet
Make sure your files follow the correct naming convention, e.g. SampleName_S1_L001_R1_001.fastq.gz (and the R2 version)
Make sure your --fastqs points to the correct location.
Make sure your --lanes, if any, are correctly specified.
Refer to the "Specifying Input FASTQs" page at https://support.10xgenomics.com/ for more details.
My code is cellranger count --id=bc --transcriptome=/home/a2433564374/public/cellranger.index/refdata-gex-GRCh38-2024-A --fastqs=/home/a2433564374/lesson/lesson1-cellranger/out --create-bam=true --sample=bc --nosecondary
I am utilizing the version 8.0.0 of CellRanger
(cellranger1) a2433564374@lizhengjian:/public/cellranger.index$ ls
refdata-gex-GRCh38-2024-A refdata-gex-GRCh38-2024-A.tar.gz
(cellranger1) a2433564374@lizhengjian:/public/cellranger.index$ cd refdata-gex-GRCh38-2024-A
(cellranger1) a2433564374@lizhengjian:/public/cellranger.index/refdata-gex-GRCh38-2024-A$ ls
fasta genes reference.json star
(cellranger1) a2433564374@lizhengjian:/public/cellranger.index/refdata-gex-GRCh38-2024-A$ pwd
/home/a2433564374/public/cellranger.index/refdata-gex-GRCh38-2024-A
(cellranger1) a2433564374@lizhengjian:/lesson/lesson1-cellranger$ cd out
(cellranger1) a2433564374@lizhengjian:/lesson/lesson1-cellranger/out$ ls
bc_S1_LOO1_R1_001.fastq.gz bc_S1_LOO1_R2_001.fastq.gz
(cellranger1) a2433564374@lizhengjian:~/lesson/lesson1-cellranger/out$ pwd
/home/a2433564374/lesson/lesson1-cellranger/out
How should I proceed to address this issue? Once again, I express gratitude for your assistance!
The text was updated successfully, but these errors were encountered:
I am grateful for your assistance. I am a novice in using cellranger. While executing cellranger count, I encountered an error. Below is the error message.
ERROR: No input FASTQs were found for the requested parameters.
If your files came from bcl2fastq or mkfastq:
Refer to the "Specifying Input FASTQs" page at https://support.10xgenomics.com/ for more details.
My code is cellranger count --id=bc --transcriptome=/home/a2433564374/public/cellranger.index/refdata-gex-GRCh38-2024-A --fastqs=/home/a2433564374/lesson/lesson1-cellranger/out --create-bam=true --sample=bc --nosecondary
I am utilizing the version 8.0.0 of CellRanger
(cellranger1) a2433564374@lizhengjian:
/public/cellranger.index$ ls/public/cellranger.index$ cd refdata-gex-GRCh38-2024-Arefdata-gex-GRCh38-2024-A refdata-gex-GRCh38-2024-A.tar.gz
(cellranger1) a2433564374@lizhengjian:
(cellranger1) a2433564374@lizhengjian:
/public/cellranger.index/refdata-gex-GRCh38-2024-A$ ls/public/cellranger.index/refdata-gex-GRCh38-2024-A$ pwdfasta genes reference.json star
(cellranger1) a2433564374@lizhengjian:
/home/a2433564374/public/cellranger.index/refdata-gex-GRCh38-2024-A
(cellranger1) a2433564374@lizhengjian:
/lesson/lesson1-cellranger$ cd out/lesson/lesson1-cellranger/out$ ls(cellranger1) a2433564374@lizhengjian:
bc_S1_LOO1_R1_001.fastq.gz bc_S1_LOO1_R2_001.fastq.gz
(cellranger1) a2433564374@lizhengjian:~/lesson/lesson1-cellranger/out$ pwd
/home/a2433564374/lesson/lesson1-cellranger/out
How should I proceed to address this issue? Once again, I express gratitude for your assistance!
The text was updated successfully, but these errors were encountered: