10 x Genomics 3'

cellranger mkref -h

Prepare a reference for use with 10x analysis software. Requires a GTF and FASTA

Usage: cellranger mkref [OPTIONS] --genome <GENOME_NAMES> --fasta <FASTA_FILES> --genes <GTF_FILES>

Options:
      --genome <GENOME_NAMES>      Unique genome name, used to name output folder [a-zA-Z0-9_-]+. Specify multiple genomes by specifying this argument
                                   multiple times; the output folder will be <name1>_and_<name2>
      --fasta <FASTA_FILES>        Path to FASTA file containing your genome reference. Specify multiple genomes by specifying this argument multiple times
      --genes <GTF_FILES>          Path to genes GTF file containing annotated genes for your genome reference. Specify multiple genomes by specifying this
                                   argument multiple times
      --nthreads <NUM_THREADS>     Number of threads used during STAR genome index generation. Defaults to 1 [default: 1]
      --memgb <MEM_GB>             Maximum memory (GB) used [default: 16]
      --ref-version <REF_VERSION>  Optional reference version string to include with reference
      --dry                        Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop
      --jobmode <MODE>             Job manager to use. Valid options: local (default), sge, lsf, slurm or path to a .template file. Search for help on
                                   "Cluster Mode" at support.10xgenomics.com for more details on configuring the pipeline to use a compute cluster
      --localcores <NUM>           Set max cores the pipeline may request at one time. Only applies to local jobs
      --localmem <NUM>             Set max GB the pipeline may request at one time. Only applies to local jobs
      --localvmem <NUM>            Set max virtual address space in GB for the pipeline. Only applies to local jobs
      --mempercore <NUM>           Reserve enough threads for each job to ensure enough memory will be available, assuming each core on your cluster has at
                                   least this much memory available. Only applies to cluster jobmodes
      --maxjobs <NUM>              Set max jobs submitted to cluster at one time. Only applies to cluster jobmodes
      --jobinterval <NUM>          Set delay between submitting jobs to cluster, in ms. Only applies to cluster jobmodes
      --overrides <PATH>           The path to a JSON file that specifies stage-level overrides for cores and memory. Finer-grained than --localcores,
                                   --mempercore and --localmem. Consult https://support.10xgenomics.com/ for an example override file
      --output-dir <PATH>          Output the results to this directory
      --uiport <PORT>              Serve web UI at http://localhost:PORT
      --disable-ui                 Do not serve the web UI
      --noexit                     Keep web UI running after pipestance completes or fails
      --nopreflight                Skip preflight checks
  -h, --help                       Print help

export PATH=/work/home/acwnw4bl7y/cellranger-8.0.1/bin:$PATH
cellranger mkref \
  --genome=Rattus_norvegicus \
  --output-dir=/work/home/acwnw4bl7y/Rat \
  --nthreads=32 \
  --memgb=64 \
 --fasta=/work/home/acwnw4bl7y/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa \
 --genes=/work/home/acwnw4bl7y/Rattus_norvegicus.mRatBN7.2.109.gtf 

参考资料：

Build a Custom Reference for Cell Ranger (mkref) - Official 10x Genomics Support
利用cellranger对（人）单细胞数据进行上游分析(实验室日记day1和day2)_cellranger mkref-CSDN博客