createSizeSelectedEnsemblncRNADB: Generate ncRNA database for rnastarMapping

Description Usage Arguments Value

View source: R/RNASeqUtility.R

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

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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 10, 2017, 1:41 p.m.