Index targets

Bowtie index targets

index_targets(
  targets,
  bsgenome = getBSgenome(genome(targets)[1]),
  outdir = OUTDIR,
  verbose = TRUE
)

Arguments

targets	GRanges-class
bsgenome	BSgenome-class
outdir	string: output directory
verbose	TRUE (default) or FALSE

Value

invisible(targetdir)

Examples

require(magrittr)
bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
bedfile  <- system.file('extdata/SRF.bed', package = 'multicrispr')
targets <- extend(bed_to_granges(bedfile, genome = 'mm10'))
#> 	Read SRF.bed into GRanges
#> 		1974 ranges on 21 chromosomes
index_targets(targets, bsgenome)
#> 	Index target sequences
#> 		1974 target ranges
#> 		3932 ranges after merging overlaps
#> 		Write seqs  to ~/multicrisprout/targets.fa
#> 		Write index to ~/multicrisprout/targets