Index genome — index_genome • multicrispr

Bowtie index genome

index_genome(
  bsgenome,
  indexedgenomesdir = INDEXEDGENOMESDIR,
  download = TRUE,
  overwrite = FALSE
)

Arguments

bsgenome	`BSgenome-class`
indexedgenomesdir	string: directory with bowtie-indexed genome
download	TRUE (default) or FALSE: whether to download pre-indexed version if available
overwrite	TRUE or FALSE (default)

Value

invisible(genomdir)

Details

Checks whether already available locally. If not, checks whether indexed version can be downloaded from our s3 storage. If not, builds the index with bowtie. This can take a few hours, but is a one-time operation.

Examples

bsgenome <- BSgenome.Scerevisiae.UCSC.sacCer1::Scerevisiae
index_genome(bsgenome, indexedgenomesdir = tempdir())
#> 	Index BSgenome.Scerevisiae.UCSC.sacCer1
#> writing chr1 sequence to file ... OK
#> writing chr2 sequence to file ... OK
#> writing chr3 sequence to file ... OK
#> writing chr4 sequence to file ... OK
#> writing chr5 sequence to file ... OK
#> writing chr6 sequence to file ... OK
#> writing chr7 sequence to file ... OK
#> writing chr8 sequence to file ... OK
#> writing chr9 sequence to file ... OK
#> writing chr10 sequence to file ... OK
#> writing chr11 sequence to file ... OK
#> writing chr12 sequence to file ... OK
#> writing chr13 sequence to file ... OK
#> writing chr14 sequence to file ... OK
#> writing chr15 sequence to file ... OK
#> writing chr16 sequence to file ... OK
#> writing chrM sequence to file ... OK