build_index: Build index for mapping using Salmon

In GREP2: GEO RNA-Seq Experiments Processing Pipeline

Description

build_index for mapping reads using Salmon.

Usage

build_index(species = c("human", "mouse", "rat"), kmer = 31,
  ens_release = 92, destdir)

Arguments

species	name of the species. Only 'human', 'mouse', and 'rat' are allowed to use.
kmer	k-mer size for indexing. default is 31. See 'Salmon' for details.
ens_release	version of Ensembl release.
destdir	directory where all the files will be saved.

Value

directory of index files

References

Rob Patro, Geet Duggal, Michael I. Love, Rafael A. Irizarry, and Carl Kingsford (2017): Salmon provides fast and bias-aware https://www.nature.com/articles/nmeth.4197

Examples

#Running this function will take some time.

build_index(species="human",kmer=31,
ens_release=92,destdir=tempdir())

GREP2 documentation built on Sept. 3, 2019, 9:05 a.m.