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It should be nice to understand why always obtain NULL when using Rbowtie2 functions. The program its located in the library but it doesn´t work
library(Rbowtie2)
> td <- tempdir()
> refs <- dir(system.file(package="Rbowtie2", "extdata", "bt2","refs"),full=TRUE)
> (cmdout<-bowtie2_build(references=refs,
+ bt2Index=file.path(td, "lambda_virus"), "--threads 4 --quiet",
+ overwrite=TRUE))
NULL
I am having the same problem. Did you find a solution?