As I run the Cellranger count, I get the following error: "The argument '--fastqs <PATH-CodePudding

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.

CodePudding user response：

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:

either you want a space, but then don't put a =, as in --fastqs /home/.../pbmc_1k_v3_fastqs;
or you put an equal sign, but then don't put a space, as in --fastqs=/home/.../pbmc_1k_v3_fastqs.

CodePudding user response：

I had the same issue so I suppressed the space but now it is saying that: $ cellranger count --id=run_count_1kpbmcs \

--fastqs=/home/hd/hd_hd/hd_ak282/yard/run_cellranger_count/pbmc_1k_v3_fastqs
--sample=pbmc_1k_v3
--transcriptome=/home/hd/hd_hd/hd_ak282/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0 error: The following required arguments were not provided: --transcriptome

Can someone help me please? :)