[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?

Thanks,

Wei
________________________________
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.

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
>


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]]



More information about the Bioc-devel mailing list