getCellRangerGEXReference: Build CellRanger index

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Build CellRanger index

Description

Build CellRanger GEX or VDJ index

Usage

  getCellRangerGEXReference(param)
  getCellRangerVDJReference(param)

Arguments

param

list from ezParam .

Value

character(1): path of index.

Author(s)

Ge Tan

Examples

setwd("/scratch/gtan/dev/quickdev")
param = list()
param[['cores']] = '8'
param[['refBuild']] = 'Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26'
param[['refFeatureFile']] = 'genes.gtf'
param[['transcriptTypes']] = 'protein_coding,rRNA,tRNA,Mt_rRNA,Mt_tRNA'
param[['TenXLibrary']] = 'GEX'
param[['scMode']] = 'SC'
param <- ezParam(param)
getCellRangerGEXReference(param)

setwd("/scratch/gtan/dev/quickdev")
param = list()
param[['cores']] = '8'
param[['refBuild']] = 'Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26'
param[['refFeatureFile']] = 'genes.gtf'
param[['transcriptTypes']] = 'protein_coding,rRNA,tRNA,Mt_rRNA,Mt_tRNA'
param[['TenXLibrary']] = 'GEX'
param[['scMode']] = 'SN'
param <- ezParam(param)
getCellRangerGEXReference(param)

setwd("/scratch/gtan/dev/quickdev")
param = list()
param[['cores']] = '8'
param[['refBuild']] = 'Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26'
param[['refFeatureFile']] = 'genes.gtf'
param[['transcriptTypes']] = 'protein_coding,rRNA,tRNA,Mt_rRNA,Mt_tRNA'
param[['TenXLibrary']] = 'VDJ'
param <- ezParam(param)
getCellRangerVDJReference(param)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.