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

Wei Shi shi at wehi.edu.au
Sun Nov 26 09:41:14 CET 2017

Thanks Martin.

Ioannis: could you please provide your command and screen output from the mapping so I can try to see what might cause the long running time?


From: Martin Morgan <martin.morgan at roswellpark.org>
Sent: Sunday, November 26, 2017 2:13:43 PM
To: Ioannis Vardaxis; A.E.S.; Ryan Thompson
Cc: bioc-devel at r-project.org; Wei Shi
Subject: Re: [Bioc-devel] Question about external algorithms to Bioconductor package

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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