bowtie2-build {Rbowtie2} | R Documentation |
This function can be use to call the bowtie2-build wrapper which
wraps the bowtie2-build-s
and the bowtie2-build-l
binaries.
bowtie2_build(references, bt2Index, ..., overwrite = FALSE)
references |
|
bt2Index |
|
... |
Additional arguments to be passed on to the binaries. See below for details. |
overwrite |
|
All additional arguments in ... are interpreted as additional
parameters to be passed on to bowtie2_build wrapper. All of them should be
Character
or Numeric
scalar. You can put all additional
arguments in one Character
(e.g. "–threads 8 –quiet") with white
space separation, or put them in different Character
(e.g. "–threads","8","–quiet"). See the output of bowtie2_build_usage()
for details about available parameters.
An invisible Integer
of call status.
The value is 0 when there is not any mistakes
Otherwise the value is non-zero.
Zheng Wei
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.
td <- tempdir() ## Building a bowtie2 index refs <- dir(system.file(package="Rbowtie2", "extdata", "bt2","refs"), full=TRUE) bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"), "--threads 4 --quiet",overwrite=TRUE) ## Use additional arguments in another way bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"), "--threads",4,"--quiet",overwrite=TRUE) ## The function will print the output during the process without "--quiet" argument. bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"), overwrite=TRUE)