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?
Thanks,
Wei
________________________________
From: Martin Morgan <martin.mor...@roswellpark.org>
Sent: Sunday, November 26, 2017 2:13:43 PM
To: Ioannis Vardaxis; A.E.S.; Ryan Thompson
Cc: bioc-devel@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.
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 don�t see any reason
> using it, and this is a big problem if I cannot use bowtie inside a
> bioconductor package.
>
> Thanks
>
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
