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Hi,
Is it possible to upload BSgenome/GenomicFeatures packages for new genome assemblies of non-model species?
I assembled these genomes and had to create the BSgenome package as it was required for a different tool that I wanted to use. Interestingly, no annotation data was able for this species, which makes me think that it would be helpful for researches working with this species to have these resources.
In case, it is possible to share these resources through bioconductor, could you please share the guidelines/documentation? If it is not possible to share these annotations through bioconductor, then are there other standard strategies for sharing these resources?
Thanks in advance for the help.
Best Manish
Hi Manish,
What assembly is this about? Is it on NCBI? Almost all of the 100+ BSgenome data packages included in Bioconductor were made internally and are maintained by us. With very few exceptions where the package is an external contribution.
FWIW the process of forging a BSgenome data package has been greatly simplified in BioC 3.17. In particular, for an NCBI or UCSC assembly, there's no need to prepare a "seed file" anymore. The new tools are in the new BSgenomeForge package. This should make it easy enough for people to forge a BSgenone data package for their non-model NCBI or UCSC organism.
Best,
H.
Hi Herve,
The assembly is for apricot (Prunus armeniaca). It is not on NCBI yet but will be uploaded there soon. Indeed the process for generating the BSgenome package was easy and I could do that.
I am more curious about the 'sharing' aspect. Based on your reply, am I correct to assume that the recommendation is that users who want to use this assembly generate the BSgenome data package themselves (and individually) using the NCBI/UCSC assembly?
Best Manish
Once the assembly is on NCBI it will be trivial for anybody who wants to use it in Bioconductor to make the BSgenome data package with
BSgenomeForge::forgeBSgenomeDataPkgFromNCBI(). It is so easy that there's not much value in adding the package to the Bioconductor repositories.Note that we would consider doing so if there was something special about it, e.g. the package is hard to make and/or there's a lot of demand for it, but none of this seems to apply in the case of Prunus armeniaca. But hey, I love apricots ;-)
Cheers,
H.
Thanks for the info. This is very helpful. -Manish