I am trying to perform a cellranger count on fastq files generated from a 10x genomics single cell RNA Seq run.
Just to provide some background, I ssh’d into the AWS using our AWS IP with MobaXTerm linux command line.
My files are in the Isilon. The file folders are
path/to/runs/ - this folder contains the
.fastq files for each sample (ex:
SI_GA_D1_S4). I can see these folders listed in the linux command line.
The cellranger is found when I write the following:
ls brings up 13 items located in the folder, one of them being
When I write the following command,
/path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger count \ --id=run2\ --transcriptome=/path/to/refseq/refdata-cellranger-hg19-3.0.0\ --sample=sample1\ --expect-cells=5000
and it gives me:
-bash: /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger: No such file or directory
This looks correct from what the 10x website says for single cell RNA Seq. Please advise.
$ ls -l /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger -rwxrwx--- 1 1003080 1000000 460 Dec 5 19:41 /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger