I am trying to run cellranger count go generate count matrix for the sequenced fastq on NextSeq 500. My fastqs are named like:
SRR12345671.fastq.gz SRR12345672.fastq.gz SRR12345673.fastq.gz SRR12345674.fastq.gz SRR12345675.fastq.gz
I am using following command:
cellranger count --id=SRR1234567 --fastqs=/home/user/cellranger_count/fastqs --sample=SRR1234567 --transcriptome=/mnt/home/user/run-cellranger/refdata-cellranger-GRCh38-3.0.0
but getting the following error as:
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.
Please help me to fix this.