Cellranger count with error information “… which wasn’t expected, or isn’t valid in this context”

Cellranger count with error information “… which wasn’t expected, or isn’t valid in this context”

1

Hello everyone,

I just practiced the scRNAseq upstream analysis from cellranger official tutorial.

But I met a small problem but it stopped me from going the next step.

I followed the tutorial exactly but the error information still exist:

##
cellranger count --id=run_count_1kpbmcs \
   --fastqs=/home/user/Desktop/run_cellranger_count/pbmc_1k_v3_fastqs \
   --sample=pbmc_1k_v3 \
   --transcriptome= /home/user/Desktop/run_cellranger_count/refdata-gex-GRCh38-2020-A

error: Found argument '/home/user/Desktop/run_cellranger_count/refdata-gex-GRCh38-2020-A' which wasn't expected, or isn't valid in this context

USAGE:
    cellranger count [OPTIONS] --id <ID> --transcriptome <PATH>

For more information try --help

I tried many methods but I didn’t know what’s wrong with it .

Can somebody help me solve this problem. I’d be appreciate it.


count


cellranger


scRNAseq

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