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