build_index: Build index for mapping using Salmon

In anilchalisey/rseqR: RNA-seq data processing pipeline

Description

build_index for mapping reads using Salmon.

Usage

build_index(species = c("human", "mouse"), kmer = 31,
  ens_release = 93, dest.dir)

Arguments

species	character string specifying the name of the species. Only 'human', and 'mouse' are supported at present. [DEFAULT = human].
kmer	k-mer size for indexing. default is 31. See 'Salmon' for details.
ens_release	version of Ensembl release.
dest.dir	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 quantification of transcript expression. Nature methods, 14(4),417. https://www.nature.com/articles/nmeth.4197

anilchalisey/rseqR documentation built on May 25, 2019, 2:25 p.m.