[Bioc-devel] Question about external algorithms to Bioconductor package

Martin Morgan martin.morgan at roswellpark.org
Fri Nov 24 19:27:31 CET 2017

On 11/24/2017 01:25 PM, Ioannis Vardaxis wrote:
> Hei,
> Both kalliston and salmon er for RNA data, I have DNA data. Is there any
> other solution rather than Rsubread which is extremely slow?
> I am making an algorithm where one of its steps should be to map the DNA
> reads to the reference genome. So I would like for the user-convenience to
> do it in my algorithm. But if I cannot use anything else than Rsubread
> then I might write that the user at this point has to run bowtie with the

As I said there are two implementations of bowtie in Bioconductor; if 
that's your preferred aligner then why not use them, from within R?


> given command and then return to the package. However I try to avoid that
> if possible.
> Ioannis

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