Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

; suggestion of settable seqlevels on TwoBitFile. >>> >>> Martin >>> >>> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Rainer >>> Johannes [johannes.rai...@eurac.edu] >>> Sent:

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

ynamically remap the seqlevels when the >>>> 2bit file is loaded by AnnotationHub, which would require Herve's >>>> suggestion of settable seqlevels on TwoBitFile. >>>> >>>> Martin >>>> >>>&g

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

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] Problem with seqnames of TwoBitFile

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

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 TwoBitFile from

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

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

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

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,

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

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

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

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

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

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

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

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

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

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