.org>>
Cc: "A.E.S."
mailto:adrian.salat...@conicet.gov.ar>>, Ryan
Thompson mailto:r...@thompsonclan.org>>,
"bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>"
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Question about ext
Date: Sunday, November 26, 2017 at 9:30 PM
To: Martin Morgan
Cc: "A.E.S." , Ryan Thompson
, "bioc-devel@r-project.org" ,
Wei Shi
Subject: Re: [Bioc-devel] Question about external algorithms to Bioconductor
package
I used Rbowtie and the mapping was done in 7 minutes, the res
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
mailto:mar
.; 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;
Good day,
> I have DNA data. Is there any other solution rather than Rsubread which is
> extremely slow?
How much of it do you have? If it's a large size, such as whole genome
sequencing, then it would take longer than an RNA-seq experiment regardless of
the algorithm you use. I have used Rsub
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 mappin
On 11/24/2017 01:25 PM, Ioannis Vardaxis wrote:
Hei,
Both kalliston and salmon er for RNA data, I have DNA data. Is there any
other solution rather than Rsubread which is extremely slow?
I am making an algorithm where one of its steps should be to map the DNA
reads to the reference genome. So I
Maybe gmapR?
2017-11-24 16:25 GMT-02:00 Ioannis Vardaxis :
> Hei,
>
> Both kalliston and salmon er for RNA data, I have DNA data. Is there any
> other solution rather than Rsubread which is extremely slow?
> I am making an algorithm where one of its steps should be to map the DNA
> reads to the r
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 speedi
Hei,
Both kalliston and salmon er for RNA data, I have DNA data. Is there any
other solution rather than Rsubread which is extremely slow?
I am making an algorithm where one of its steps should be to map the DNA
reads to the reference genome. So I would like for the user-convenience to
do it in my
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
usi
On Sun, 12 Nov 2017 22:22:56 +
Ryan Thompson wrote:
> Hi,
>
> I don't know the Bioconductor policy for packages that rely on
> external tools, but for the specific features you mention, there are
> Bioconductor packages to accomplish most or all of them. You can use
> samtools via Rsamtools,
Hi,
I don't know the Bioconductor policy for packages that rely on external
tools, but for the specific features you mention, there are Bioconductor
packages to accomplish most or all of them. You can use samtools via
Rsamtools, you can use the Rsubread package in place of bowtie for
alignment, an
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