I am currently trying to run CellRanger using a custom reference build (Human genome + virus genome). I used the well explained guide on official website to do it (_mkref --genome=id_human --fasta=genome_Human.fa --genes=Human.gtf --genome=idvirus --fasta=Virus.fa --genes=Virus.gtf) . No warning were identified with the mkref module ("Reference successfully created") but when i ran count module an error raised at the checking reference path ([error] Your reference doesn't appear to be indexed. Please run the mkreference tool). The input path was the full path of the directory created by the mkref module.
I had not this error when i have separately launched count module with Human genome and the virus genome.
Edit: I don't know what was going on but it has been resolved by running again mkref with filtered version of human genome from 10X build.
Hi,
I am currently trying to run CellRanger using a custom reference build (Human genome + virus genome). I used the well explained guide on official website to do it (_mkref --genome=id_human --fasta=genome_Human.fa --genes=Human.gtf --genome=idvirus --fasta=Virus.fa --genes=Virus.gtf) . No warning were identified with the mkref module ("Reference successfully created") but when i ran count module an error raised at the checking reference path ([error] Your reference doesn't appear to be indexed. Please run the mkreference tool). The input path was the full path of the directory created by the mkref module.
I had not this error when i have separately launched count module with Human genome and the virus genome.
Edit: I don't know what was going on but it has been resolved by running again mkref with filtered version of human genome from 10X build.
Best, Wes