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Run cellranger‐arc

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chenweng1991 edited this page Jul 17, 2023 · 6 revisions

Run a minimum cellranger-arc

First, if ReDeeM experimental protocol are followed, and folders are created following Organize ReDeeM full data, Follow the command below to run cellranger

  1. Go to the folder cellranger within the working directory
sample/
├── CellRanger *
├── FASTQ
│   ├── ATAC
│   ├── Mito
│   └── RNA
└── Mito
    ├── Enrich
    └── WholeATAC
  1. Download REDEEM-V git clone https://github.com/chenweng1991/REDEEM-V.git
  2. Assign path REDEEM=ThePathToREDEEM-V #The loacation where the REDEEM-V is downloaded to
  3. Run the commands below
$REDEEM/PrepData/makelibrary.sh # Run this inside the CellRanger folder. This will create a file called "Libraries"

## Below run cell ranger
cellranger_path=Your_Path_To_cellranger-arc  #~/Cellranger-arc/cellranger-arc-2.0.0/cellranger-arc
ref=Your_Path_To_refdata-cellranger-arc-GRCh38-2020-A  #/lab/solexa_weissman/cweng/Genomes/10X/refdata-cellranger-arc-GRCh38-2020-A/
Prefix=`dirname $(pwd) | xargs basename
bsub -R "rusage[mem=200000]" $cellranger_path  count --id=$Prefix --reference=$ref --libraries=Libraries --localcores=32 --localmem=128
# Note: the bsub -R "rusage[mem=200000]" can be replaced by your cluster system. Or just delete to run locally
# --localcores=32 --localmem=128 needs to be adjusted based on your system
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