cellrangerIndexing: Cellranger indexing

In kendomaniac/CASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

Cellranger indexing

Description

This function creates the indexing for 10Xgenomics

Usage

cellrangerIndexing(
  group = c("sudo", "docker"),
  scratch.folder,
  genomeFolder,
  gtf.url,
  fasta.url,
  bio.type = c("protein_coding", "unitary_pseudogene", "unprocessed_pseudogene",
    "processed_pseudogene", "transcribed_unprocessed_pseudogene", "processed_transcript",
    "antisense", "transcribed_unitary_pseudogene", "polymorphic_pseudogene", "lincRNA",
    "sense_intronic", "transcribed_processed_pseudogene", "sense_overlapping",
    "IG_V_pseudogene", "pseudogene", "TR_V_gene", "3prime_overlapping_ncRNA",
    "IG_V_gene", "bidirectional_promoter_lncRNA", "snRNA", "miRNA", "misc_RNA", "snoRNA",
    "rRNA", "IG_C_gene", "IG_J_gene", 
     "TR_J_gene", "TR_C_gene", "TR_V_pseudogene",
    "TR_J_pseudogene", "IG_D_gene", "ribozyme", "IG_C_pseudogene", "TR_D_gene", "TEC",
    "IG_J_pseudogene", "scRNA", "scaRNA", "vaultRNA", "sRNA", "macro_lncRNA",
    "non_coding", "IG_pseudogene"),
  nThreads,
  version = "5"
)

Arguments

group,	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder,	a character string indicating the path of the scratch folder
genomeFolder,	path for the genome folder
gtf.url,	a character string indicating the URL from ENSEMBL ftp for the GTF for genome of interest
fasta.url,	a character string indicating the URL from ENSEMBL ftp for the unmasked genome sequence of interest
bio.type,	ENSEMBL biotype to filter the GTF
nThreads,	number of cores for parallelization
version,	cellranger version: 2, 3 or 5.

Value

an indexed genome compliant with 10XGenomics cellranger

Author(s)

Luca Alessandrì

Examples

## Not run: 
library(rCASC)
setwd("/data/genomes/hg38refcellranger")

cellrangerIndexing(group="docker", scratch.folder="/data/scratch", 
            gtf.url="ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz",
            fasta.url="ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz",
            genomeFolder = getwd(), bio.type="protein_coding", nThreads = 8)

## End(Not run)

kendomaniac/CASC documentation built on Oct. 4, 2023, 11:10 a.m.