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

[Ioannis Vardaxis]

I used Rbowtie and the mapping was done in 7 minutes, the results where fine too. Rsubread had been running for 2 days so I had to stop it.
But anyway I can use Rbowtie which is nice :)


Ioannis Vardaxis
Stipendiat NTNU
Sendt fra min iPhone

26. nov. 2017 kl. 04:14 skrev Martin Morgan <martin.morgan at roswellpark.org<mailto:martin.morgan at roswellpark.org>>:

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.

Martin

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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