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

[Benilton Carvalho]

Maybe gmapR?

2017-11-24 16:25 GMT-02:00 Ioannis Vardaxis <ioannis.vardaxis at ntnu.no>:

> 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
> given command and then return to the package. However I try to avoid that
> if possible.
>
> Ioannis
> --
> Ioannis Vardaxis
>
> Stipendiat IMF
> NTNU
>
>
>
>
> On 24/11/2017, 19:11, "Martin Morgan" <martin.morgan at roswellpark.org>
> wrote:
>
> >On 11/24/2017 09:57 AM, Ioannis Vardaxis wrote:
> >> Hi,
> >>
> >> I tried the Rsubread package you suggested and the mapping is running.
> >> However it takes like forever to end. Even in parallel it needs some
> >>days
> >> to run while bowtie for example needs only a couple of hours in 4 cores.
> >> Is there any way of speeding up Rsubread? Or else I don¹t see any reason
> >> using it, and this is a big problem if I cannot use bowtie inside a
> >> bioconductor package.
> >
> >I'm not following this thread closely but there are two Bowtie
> >implementations in Bioconductor
> >
> >http://bioconductor.org/packages/release/bioc/html/Rbowtie.html
> >http://bioconductor.org/packages/release/bioc/html/Rbowtie2.html
> >
> >The fast solution for many problems (mapping to known transcripts) is
> >kalisto / salmon, which are not available in Bioconductor -- integrating
> >either of these as _libraries_ would be a nice package.
> >
> >Martin
> >
> >
> >>
> >> Thanks
> >>
> >
> >
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