A function to create a genome index for indrop V2 single cell data

This function executes a docker that produces as output the genome index index for bowtie

indropIndex(
  group = c("sudo", "docker"),
  index.folder,
  ensembl.urlgenome,
  ensembl.urlgtf
)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

index.folder,

a character string indicating the folder where the index will be created. The index will have the prefix genome.

ensembl.urlgenome,

a character string indicating the URL from ENSEMBL ftp for the unmasked genome sequence of interest

ensembl.urlgtf,

a character string indicating the URL from ENSEMBL ftp for the GTF for genome of interest

Author

Raffaele Calogero and Riccardo Panero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit, University of Torino Italy

Examples

if (FALSE) {
library(rCASC)
#running indropCounts index build
indropIndex(group="docker", index.folder=getwd(),
    ensembl.urlgenome="ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz",
    ensembl.urlgtf="ftp://ftp.ensembl.org/pub/release-87/gtf/mus_musculus/Mus_musculus.GRCm38.87.gtf.gz")
}