s) to make the
>>>> seqlevels sensible on the way in to annotation hub; this is against Sean's
>>>> advice and I'm not really a big fan of this.
>>>>
>>>> I like the idea of being able to dynamically remap the seqlevels when the
>>>
way in to annotation hub; this is against Sean's
>>> advice and I'm not really a big fan of this.
>>>
>>> I like the idea of being able to dynamically remap the seqlevels when the
>>> 2bit file is loaded by AnnotationHub, which would require Herve's
>>> sugge
itFile.
Martin
From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Rainer
Johannes [johannes.rai...@eurac.edu]
Sent: Saturday, January 09, 2016 11:01 AM
To: Hervé Pagès
Cc: Michael Lawrence; Martin Morgan
Subject: Re: [Bioc-devel] Problem with seq
Also things like organismdbi don't seem to exist for organisms other than
human, mouse, rat. So if you want to use that infrastructure for fly or worms,
you're SOL at the moment.
This is a highly topical discussion since many/most microarray probes can be
profitably (in terms of knowledge, no
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Rainer
> Johannes [johannes.rai...@eurac.edu]
> Sent: Saturday, January 09, 2016 11:01 AM
> To: Hervé Pagès
> Cc: Michael Lawrence; Martin Morgan
> Subject: Re: [Bioc-devel] Problem with seqnames of Tw
le seqlevels on TwoBitFile.
Martin
From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Rainer
Johannes [johannes.rai...@eurac.edu]
Sent: Saturday, January 09, 2016 11:01 AM
To: Hervé Pagès
Cc: Michael Lawrence; Martin Morgan
Subject: Re: [Bioc-devel] Probl
Yes, using BSGenome would help in this case.
In the long run I think it might be important to have this fixed, not
necessarily for human, but for other species/genome builds for which there
might not be an BSGenome package available; through AnnotationHub all GTF files
and fasta files would be
On 01/08/2016 01:09 PM, Michael Lawrence wrote:
That is one solution. But everyone using that genome would need to
reset the seqlevels to the "standard" ones. In this specific case, is
there any reason not to just use the BSgenome for GRCh38?
I agree. Maybe we don't need seqlevels<-,TwoBitFile
That is one solution. But everyone using that genome would need to
reset the seqlevels to the "standard" ones. In this specific case, is
there any reason not to just use the BSgenome for GRCh38?
On Fri, Jan 8, 2016 at 11:04 AM, Hervé Pagès wrote:
> Hi Jo, Michael,
>
> What about implementing a se
Hi Jo, Michael,
What about implementing a seqlevels() setter for TwoBitFile objects? All
you need for this is an extra slot for storing the user-supplied
seqlevels. Note that in general the seqlevels() setter allows more than
renaming the seqlevels. It also allows dropping, adding, and shuffling
I agree, I would not modify the file content. At present it is however not
possible to use e.g. getSeq on these TwoBitFiles, since the chromosome names in
the submitted GRanges (e.g. 1) do not match the seqnames/seqinfo of the
TwoBitFile. I don’t know if a seqnames or seqinfo method stripping of
This is perhaps something that could be handled when population the
hub, but I'm not sure how rtracklayer could automatically derive the
chromosome names.
On Fri, Jan 8, 2016 at 2:37 AM, Rainer Johannes
wrote:
> dear all,
>
> I just run into a problem with a TwoBitFile I fetched from AnnotationHu
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