[Bioc-devel] Phase 3 1000 genomes reference genome
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Tue Apr 20 22:26:19 CEST 2021
On 4/16/21 4:28 AM, Murphy, Alan E wrote:
> Hi all,
> I am looking for the 1000genomes Phase3 Reference Genome Sequence (equivalent to the Phase 2 version would be useful: BSgenome.Hsapiens.1000genomes.hs37d5 https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.1000genomes.hs37d5.html). The dataset I'm looking for is also found here for download: https://ctg.cncr.nl/software/MAGMA/ref_data/g1000_eur.zip
> Is this available in Bioconductor?
I don't think we have that:
grep("1000", available.genomes(), value=TRUE)
#  "BSgenome.Hsapiens.1000genomes.hs37d5"
Note that BSgenome.Hsapiens.1000genomes.hs37d5 is a contributed package
(by Julian Gehring). You're welcome to contribute a BSgenome data
package for the 1000genomes Phase3 Reference Genome if you'd like.
> I want to use it in a package I'm developing. I know I could download it through the package when needed or store the dataset in as package data but I know neither of these solutions are not good practice for Bioconductor submission.
> Kind regards,
> Alan Murphy
> Neurogenomics lab
> UK Dementia Research Institute
> Imperial College London
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