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

Martin Morgan martin.morgan at roswellpark.org
Sun Nov 26 04:13:43 CET 2017

I think that generally Rsubread is 'fast' so you might make sure that 
there are not obvious problems, e.g., aligning reads to the wrong 
reference; maybe Wei Shi will chime in.


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.
> Thanks

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