cellranger-dna: Your reference doesn't appear to be indexed. Please run the mkref tool.

Question

[Hao]

I received the following error when running cellranger-dna: "Your reference doesn't appear to be indexed. Please run the mkref tool". The reference that I used was downloaded from 10X database.

I thought the reference was already indexed, though the error above suggests otherwise. Anyway, I ran mkref by using the command "cellranger mkref --genome=output_genome --fasta=fasta/genome.fa --genes=genes/genes.gtf --nthreads=80 --memgb=128" and then used "output_genome" as the reference for "cellranger-dna cnv" and I got the same error.

Can anyone help me with this? Thanks in advance.

Answer 1

[Hao]

I was able to get past this error with the help of this topic. Turns out the correct tool to index the fa file is "cellranger-dna mkref" and not "cellranger mkref". Anyway, there are several indexed references in the link so one will probably not need to run mkref themself.