which I think is not an
option for BioC/Rbowtie.
I hope that resolves also the issue on El Capitan.
Michael
On 19.04.2017 13:47, Martin Morgan wrote:
> On 04/19/2017 05:45 AM, Michael Stadler wrote:
>> Dear BioC core,
>>
>> Thanks for the report, Herve. If I understand correc
mething to worry about?
I hope to get back with a solution for the bowtie issue soon.
Michael
On 19.04.2017 13:47, Martin Morgan wrote:
> On 04/19/2017 05:45 AM, Michael Stadler wrote:
>> Dear BioC core,
>>
>> Thanks for the report, Herve. If I understand correctly, there
Dear BioC core,
Thanks for the report, Herve. If I understand correctly, there is
nothing I can do at this point to make QuasR green on windows, correct?
I have another question regarding QuasR not building on veracruz2: The
vignette does not build currently, reporting:
Error on veracruz2.biocond
Dear Jurat,
Maybe this would be better asked on support.bioconductor.org.
I don't think I fully understand what you intend to do (a fully working
example would help), but here are two ideas that could be useful:
1. Maybe a single findOverlaps() will be enough to find all you need:
D <- c(a,b,c)
oday and will let you know.
>>
>> H.
>>
>> On 04/30/2015 08:42 AM, Michael Stadler wrote:
>>> Hi Herve,
>>>
>>> I stumbled again over the 'memory not mapped' issue in trimLRpatterns
>>> using updated versions of R and BioC-devel.
,
>
> Thanks for the report. I'll look into this.
>
> H.
>
> On 04/22/2014 08:29 AM, Michael Stadler wrote:
>> Dear Herve,
>>
>> We are hitting a 'memory not mapped' problem when using trimLRpatterns
>> as detailed below. I did not manage t
se Rbowtie <= 1.4.4
(based on bowtie 1.0.1)
- OS X 10.9 onwards and everything else uses Rbowtie >= 1.4.5
(based on bowtie 1.0.1 /patched bugs-312).
Thanks again for your efforts,
Michael
On 14.06.2014 01:31, Dan Tenenbaum wrote:
> Hi Michael,
>
>
>
> - Original
leased, so what have you changed
> in between?
>
> Best,
> Kasper
>
>
> On Fri, Jun 13, 2014 at 3:32 AM, Michael Stadler <mailto:michael.stad...@fmi.ch>> wrote:
>
> Hi Dan,
>
> I'm cc'ing the list; maybe somebody else has experie
Hi Dan,
I'm cc'ing the list; maybe somebody else has experienced differences
between petty and perceval.
Rbowtie release (1.4.5) is not building under OS X 10.6.8 (petty).
Rbowtie release (1.4.5) and development (1.5.5) are virtually identical
(only DESCRIPTION and NEWS differ).
The development
Dear Herve,
We are hitting a 'memory not mapped' problem when using trimLRpatterns
as detailed below. I did not manage to reproduce it with few sequences,
so I have to refer to a publicly available sequence file with many
reads. Even then, it occasionally runs through without problems.
Also, our
other
> users. The new version won't become available before tomorrow though.
> But, again, this new version (1.25.18) is similar to the current
> version (1.25.17), so you can re-install now with
> biocLite("AnnotationDbi"). No need to wait until tomorrow.
>
>
Dear Bioc gurus,
Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some
unit tests, which turns out to be reproducible independent of QuasR and
might be related to R getting the wrong method for "[[<-".
The following works fine...
library(GenomicRanges)
grl <- GRangesList(r1=GRanges
I agree that the profile or metagene plot is useful and widely applied.
Creating such a plot consists of several steps, including:
- quantifying and accumulating signal around sites of interest
- normalization
- visualization
The qProfile() function in QuasR was designed to do the
quantification/
ils datasets methods
> [8] base
>
> other attached packages:
> [1] GenomicRanges_1.13.39 XVector_0.1.0 IRanges_1.19.28
> [4] BiocGenerics_0.7.4
>
> loaded via a namespace (and not attached):
> [1] stats4_3.0.1
>
>
> On 08/29/2013 08:48 AM, Michael Stadle
Dear masters of genomic ranges,
Since a few days, I am getting an error in Bioc 2.13 when comparing two
GRanges objects by setdiff():
chrs <- c(chr1=20, chr2=20)
grA <- GRanges("chr1", IRanges(1,10), strand="*", seqlengths=chrs)
grB <- GRanges("chr2", IRanges(11,15), strand="*", seqlengths=chrs)
Thanks, Davide.
That's also what I had in mind in case there is nothing more elegant to
be found.
Best,
Michael
On 29.07.2013 11:01, Davide Rambaldi IEO wrote:
> What about using already installed command line tools and parsing the output?
>
> - df (diskfree) on Linux and Mac OSX
>
> - fsutil
Dear list,
I am looking for a way to programmatically get the unused disk space in
R, ideally in a portable way that works on windows/linux/os x.
I have come across OS specific solutions for C (e.g. using statvfs for
linux), but I wonder if I am missing something simpler.
Thank you for any help,
Hi Martin,
Thank you for the quick response. Now it works like a charm.
Best wishes,
Michael
On 27.05.2013 17:29, Martin Morgan wrote:
> On 05/26/2013 11:57 PM, Michael Stadler wrote:
>> Dear bioc core developers,
>>
>> We have recently (a few months back?) started to
Dear bioc core developers,
We have recently (a few months back?) started to get error messages of
the type:
libgomp: Thread creation failed: Resource temporarily unavailable
when using ShortRead::FastqStreamer in combination with
parallel::parLapply (for example in QuasR::preprocessReads or
Quas
cked into versions 1.4.12 (release) and 1.5.44 (devel).
>
> Valerie
>
>
> On 03/07/13 05:43, Michael Stadler wrote:
>> Here is the second attachment ("variants.vcf") that was missing from the
>> first message.
>>
>> Michael
>>
>> On 03/07/2
Here is the second attachment ("variants.vcf") that was missing from the
first message.
Michael
On 03/07/2013 02:40 PM, Michael Stadler wrote:
> Dear Valerie and colleagues,
>
> I have recently started using the VariantAnnotation package, which is a
> huge asset fo
Dear Valerie and colleagues,
I have recently started using the VariantAnnotation package, which is a
huge asset for much of my work with sequence variants - thank you!
I have a question regarding the following example (it makes use of two
small text files, "annot.gtf" and "variants.vcf", attached
22 matches
Mail list logo
