Hi Julian,
many thanks for the kind explanation it was very useful.
I will use your suggestion also because I am working only with
toplevel chromosomes.
Cheers
Raf
>Hi Raffaele,
>Ignore my last post completely, it was overly optimistic:
>The 'BSgenome.Hsapiens.NCBI.GRCh38' package contains t
Hi Raffaele,
You are in luck today because while we normally do *not* have mechanisms
to harmonize the non-standard chromosome names, for this specific case
Herve wrote some code to handle it. So you want to look at this:
library(GenomeInfoDb)
?fetchExtendedChromInfoFromUCSC
Marc
On 12
Hi Raffaele,
Ignore my last post completely, it was overly optimistic:
The 'BSgenome.Hsapiens.NCBI.GRCh38' package contains the genomic
sequence that is identical between GRCh38 and hg38. The naming of the
chromosomes is different. For the toplevel chromosomes, the names can
be easily converted
Ignore my comment about the naming convention.
On Tue, Dec 2, 2014 at 15:45, Julian Gehring wrote:The naming of the
chromosomes has been harmonized between UCSC and GRCh with the new release, so
there should be no need for two versions at the genome level.
[[alternative HTML version del
Hi Raffaele,
See here:
http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.GRCh38.html
Best,
Jim
On Tue, Dec 2, 2014 at 9:10 AM, Raffaele Adolfo Calogero <
raffaele.calog...@unito.it> wrote:
> Dear Bioc Team,
> I am the maintainer of chimera package.
> Recen
Hi Raffaele,
You can find it under the name
BSgenome.Hsapiens.NCBI.GRCh38
http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.GRCh38.html
(http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.GRCh38.html)
The naming of the chr
Dear Bioc Team,
I am the maintainer of chimera package.
Recently some of the users asked for the possibility to use chimera with
fusions detected on hg38 human genome.
I checked for the availability of hg38 as BSgenome but I did not find it in
Bioc repository, as instead there is TxDb.Hsapiens.UCSC
