buildBowtie2BuildCommandLine | R Documentation |
Construct a Bowtie2-build command line that can create a Bowtie2 index file.
buildBowtie2BuildCommandLine(inputFastaFile, outputIndexFile,
optionsFile = "Options.txt", verbose = TRUE, debug = FALSE)
inputFastaFile |
a character string that contains comma separated full pathnames to existing FASTA files |
outputIndexFile |
base name for the set of index files to be created |
optionsFile |
the options file. This invokes |
a character string, suitable for passing to callBowtie2Build
or to
system
.
This blindly assumes that the 'bowtie2-build' executable is in the same folder as 'bowtie2'.
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