/10X_ATACseq

Primary LanguageShell

scATAC

Usage

  1. install
  • Enter your information from this link
  • Install cellranger-atac using your own token&id
mkdir tools
cd tools
// Example
wget -O cellranger-atac-1.1.0.tar.gz "http://cf.10xgenomics.com/releases/cell-atac/cellranger-atac-1.1.0.tar.gz?Expires=(put your token&id)"
  • Get references if you want to get more references, see this link
qsub -l os7 -cwd path/to/install.sh

// for test
export PATH=tools/cellranger-atac-1.1.0:$PATH
cellranger-atac testrun --id=tiny
  1. run
// Example
sh path/to/run.sh -i ID_NAME -r path/to/REFERENCE -f path/to/FASTQS

directory

.
├── _code
|   ├── install.sh
|   ├── cellranger-atac.sh
|   └── run.sh
├── _tools
|   ├─ cellranger-atac-1.1.0
└── _reference
    └─ refdata-cellranger-atac-GRCh38-1.1.0