I downloaded the cell ranger reference database from wget https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0.tar.gz then I tar tar xvzf the .tar.gz file and got a refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 folder in my path.
But when I run the cell ranger count command, I got an error said: [error] Your reference does not contain the expected files, or they are not readable. Please check your reference folder on n145.
I have deleted and reinstalled the databased several times but still got the same error. Can anybody provide me some advice on this please?
Thank you very much!
2 answers
It looks to me that you downloaed the VDJ reference instead of the reference for GEX data? Since you used ""cellranger count", I assume the fastq files you have contains GEX data. Otherwise, you might want to try "cellranger vdj".
To answer myself's question: I used a vdj database for my gene expression data. So when I switch to the correct databases, it worked.
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Can you provide the complete command you are trying to use? Which specific cellranger program are you using?
Yeah I should have, Sorry about that! Here is my command:
Thanks very much!!
Maybe, you should check your cellranger version, and makesure the ref was made by the right cellranger version.