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CellRanger-ARC

Description

cellranger-arc website

The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells. Additionally, the pipelines perform secondary analyses like dimensionality reduction, clustering, differential analysis, and feature linkage between peaks and genes that aid in data interpretation. Available reference datasets: ercc92, GRCh38, hg19, hg19_and_mm10, mm10

Environment Modules

Run module spider cellranger-arc to find out what environment modules are available for this application.

Environment Variables

  • HPC_CELLRANGERARC_DIR - installation directory
  • HPC_CELLRANGERARC_BIN - executable directory
  • HPC_CELLRANGERARC_REF - reference directory

Categories

biology, ngs, rna-seq