Description Usage Arguments Support for compressed input files Known issues Author(s)
Creates index on reference genome using bowtie2-build.
1 2 3 | ## Default S3 method:
bowtie2Build(pathnameFAs, bowtieRefIndexPrefix, optionsVec=NULL, ...,
command="bowtie2-build", verbose=FALSE)
|
pathnameFAs |
A |
bowtieRefIndexPrefix |
A |
optionsVec |
(optional) A named |
... |
... |
command |
The name of the external executable. |
verbose |
See |
If gzipped FASTA files are used, this function will temporarily decompress before passing them to the bowtie2-build external software (which only support non-compressed FASTA files).
The FASTA pathnames must not contain commas. If detected, this method generates an informative error.
Henrik Bengtsson, Taku Tokuyasu
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