Question

Request : Add Chinese Spring Wheat genome to BSgenome

1

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remerandmaxence ▴ 10

@fb1210e9

Last seen 2.5 years ago

France

Hello,

The team I am currently working with is studying chinese spring wheat (Triticum aestivum) and we would greatly benefit from a common package for both the base genome and its related annotation. However when trying to forge the BSgenome package, I get an error since no current genome is registered for wheat in Bioconductor. The reference genome is available here at URGI with the associated project page from NCBI if needed. Is it possible to add this genome on Bioconductor so that I can forge the package ?

Thanks in advance !

Have a nice day :)

Maxence

BSgenome • 1.1k views

ADD COMMENT • link updated 10 months ago by eviatar.weizman • 0 • written 2.6 years ago by remerandmaxence ▴ 10

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Hi,

I am also interested in using the IWGSC CS RefSeq v2.1 genome in BSgenome. Have you been able to forge the package? If so, would it be possible to share?

Best regards, Thomas

ADD REPLY • link 22 months ago Thomas • 0

score 1 · Accepted Answer · 2022-05-09

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Hervé Pagès 16k

@herve-pages-1542

Last seen 3 days ago

Seattle, WA, United States

Hi Maxence,

I registered the IWGSC CS RefSeq v2.1 assembly in GenomeInfoDb 1.32.2 (release) and 1.33.3 (devel). These new versions should become available via BiocManager::install() in the next couple of days.

Best,

H.

ADD COMMENT • link 2.6 years ago Hervé Pagès 16k

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Hi Herve,

is the IWGC loaded to GenomeInfoDb?

    library(GenomeInfoDb) # v1.34.9
names(genomeStyles())

 [1] "Arabidopsis_thaliana"     "Caenorhabditis_elegans"   "Canis_familiaris"         "Cyanidioschyzon_merolae" 
 [5] "Drosophila_melanogaster"  "Homo_sapiens"             "Mus_musculus"             "Oryza_sativa"            
 [9] "Populus_trichocarpa"      "Rattus_norvegicus"        "Saccharomyces_cerevisiae" "Zea_mays"

Thanks, E.

ADD REPLY • link 10 months ago eviatar.weizman • 0