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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