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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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[error] Your reference doesn't appear to be indexed. Please run the mkref tool. #131

Closed lwtan90 closed 2 years ago

lwtan90 commented 2 years ago

Hi,

I am using cellranger-atac count. Also, I downloaded the precompiled reference (refdata-cellranger-arc-GRCh38-2020-A-2.0.0), and unpacked it. My cellranger-atac version is 1.1.0.

However, I am getting this error message to run mkref tool. In the fasta folder, I can clearly see .fai file which means the genome.fa has been indexed.

Is there a workaround? Thanks.

plbaldoni commented 2 years ago

I am having the same issue. It seems that the error is coming from here

lwtan90 commented 2 years ago

And they dont respond to questions?

evolvedmicrobe commented 2 years ago

Hi @lwtan90 and @plbaldoni,

For a timely response to any questions, please contact support@10xgenomics.com to get in touch with our support group. cellranger arc and cellranger atac 1.1 use different reference files, so you'll want to use the download from here instead:

https://support.10xgenomics.com/single-cell-atac/software/downloads/1.1/