I am following the 10x Cellranger steps and using the same files for cellranger count. I run this from the fastq directory that contains all the PBMCs fastq files and the GRCh38 files too.
As I run the Cellranger count, I get the following error: "The argument '--fastqs <PATH>...' requires a value but none was supplied"
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You put a space between
--fastqs=and/home/.../pbmc_1k_v3_fastqs, and thus it think you didn't provide an argument after--fastqs. There are two possible syntax:=, as in--fastqs /home/.../pbmc_1k_v3_fastqs;--fastqs=/home/.../pbmc_1k_v3_fastqs.