createSizeSelectedEnsemblncRNADB: Generate ncRNA database for rnastarMapping

In SimonSchafferer/RNASeqUtility: ncRNA RNA-Seq analysis utilities

Description

This method downloads ensembl ncRNA data if provided with ftp adress, modifies the fasta file, subsets the fasta file to sequences of a given and generates a STAR index file if wanted.

Usage

createSizeSelectedEnsemblncRNADB(genomeDBdir = "/tmp/mmu", ncRNAsize = 400,
  nrThreads = 6, ensemblFTP = "mouse", generateIdx = FALSE)

Arguments

genomeDBdir	Location to where the database should be saved
ncRNAsize	maximum sequence length of the fasta file (default 400nt)
nrThreads	Number of threads for the rnastar program (default 6)
ensemblFTP	ftp adress e.g. ftp://ftp.ensembl.org/pub/release-78/fasta/mus_musculus/ncrna/, however for convenience for mouse and human the ftp sites are stored and either 'mouse' or 'human' may be used for parametrization
generateIdx	Specification if an rnastar index should be created (default FALSE)

Value

all commands generated

SimonSchafferer/RNASeqUtility documentation built on May 9, 2019, 1:34 p.m.