Hello, 

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? 


`cellranger count` expects a certain nomenclature for the `fastq` files, please see the last section [here](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input), "My FASTQs are not named like any of the above examples".

Basically this is how your file names should look like: `[Sample Name]_S1_L00[Lane Number]_[Read Type]_001.fastq.gz`.

For the `Read Type`, you can take a look at your fastq files with `head` to see what is what. The link above explains different read types.

