computational cost
consideration.
Thanks for considering Subread and good luck for your project.
Wei
From: Bhagwat, Aditya
Sent: Saturday, November 9, 2019 8:06 pm
To: Pages, Herve; bioc-devel@r-project.org
Cc: Wei Shi; Michael Stadler (michael.stad...@fmi.ch
you can provide your command and screen output. But there
are certainly other Bioconductor packages that can do proper alignment for you.
Wei
Wei Shi, PhD
Laboratory Head
The Walter and Eliza Hall Institute of Medical Research
Melbourne, Australia
From: Ioannis Vardaxis
.; 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;
We have created a new experimental data package called 'seqc'. It includes
gene-level read count data generated by the SEQC (SEquencing Quality Control)
project, which is the third stage of the well-known MAQC project (a US FDA
initiative). The SEQC/MAQC-III Consortium produced benchmark RNA-seq
Hi Ryan,
It seems you are using a quite old version of Subread. The latest version of
SourceForge Subread is 1.4.2 and the latest version of bioc Rsubread is 1.12.3.
These indexing building issues had already been fixed.
Cheers,
Wei
On Nov 27, 2013, at 12:12 PM, Ryan C. Thompson wrote:
> Actu
that this created some problem to the I/O
> also because during the run of Rsubread there were many other I/O processes
> running.
> I run again Rsubread and I did not got any error
> Thanks for the help
> Raf
>
> On 6/2/13 1:22 AM, Wei Shi wrote:
>> Dear Raf,
>>
>&
Dear Raf,
As Martin pointed, that line seems to be the concatenation of two records. But
the second record is incomplete (it doesn't have the read identifier). It seems
more likely to be a file system problem rather than Rsubread problem. Could you
please also provide the line before the proble
and the latest Rsubread version is
1.9.7. Hope it now works on george2.
The version of R I'm using is R3.0.0rc r62427.
Best regards,
Wei
On Mar 29, 2013, at 3:08 PM, Martin Morgan wrote:
> On 03/28/2013 08:36 PM, Wei Shi wrote:
>> Dear Bioc core team,
>>
>> Our R
Dear Bioc core team,
Our Rsubead package got a build error on george2, but we could not reproduce
the error on our local linux machine. It is successfully built and installed on
our linux computer. Is it possible that you can give us more information about
what might cause this error?
Many tha
