Dear developers,
in cellranger manual, it is reported that parameters --genome, --fasta and --genes of cellranger mkref can be specified multiple times, for each of the genomes that need to be merged. However, this feature does not seem to be available in scrnaseq v2.5.1 pipeline. It looks like users can create their own reference by running cellranger mkref outside of the scrnaseq pipeline, and then run it using --cellranger_index parameter instead of --genome_fasta and --gtf parameters. However, it would be nice to have this feature integrated in the pipeline.
Best,
SM
Description of feature
Dear developers, in cellranger manual, it is reported that parameters
--genome,--fastaand--genesofcellranger mkrefcan be specified multiple times, for each of the genomes that need to be merged. However, this feature does not seem to be available in scrnaseq v2.5.1 pipeline. It looks like users can create their own reference by runningcellranger mkrefoutside of the scrnaseq pipeline, and then run it using--cellranger_indexparameter instead of--genome_fastaand--gtfparameters. However, it would be nice to have this feature integrated in the pipeline. Best, SM