processing fastq files using cellranger on linux 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_A1_S1, SI_GA_B1_S2, SI_GA_C1_S3, and SI_GA_D1_S4). I can see these folders listed in the linux command line.

The cellranger is found when I write the following: 

path/to/cellranger-3.0.1/cellranger-3.0.1


then ls brings up 13 items located in the folder, one of them being cellranger.

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
this has been resolved. I downloaded the windows file and this caused trouble but when downloading the file within the Linux, it seems to be working.