I am trying to analyze the public dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126030 I've downloaded the fastq files onto my cluster, and would like to proceed with cellranger count.
I am in a test folder and the only file is: SRR8526547_1.fastq and refdata-cellranger-GRCh38-1.2.0
cellranger count --id=cellranger \ --transcriptome=/home/jl2/scratch60/refdata-cellranger-GRCh38-1.2.0/ \ --fastqs=.\ --sample=SRR8526547_1.fastq \
I keep getting the error of
Invalid path/prefix combination: /gpfs/ycga/scratch60/k/jl2/test, ['SRR8526547_1.fastq'] No input FASTQs were found for the requested parameters.
Can't seem to figure out what's wrong. Does it need fastq.gz instead of fastq?