Hi Alan,
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:
library(BSgenome)
grep("1000", available.genomes(), value=TRUE)
# [1] "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.
Best,
H.
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.
Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London
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