Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
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Lucky • 0
@lucky-24920
Last seen 5 months ago

Hello

I did the alignment with the my Chip data with latest version of mouse genome from ensemble Mouse ensemble ref, how can use ChIPAnno package for this genome version, in the R work flow we have load library of Ensdb as mentioned. If google for mouse db I am getting latest version of library for mouse is EnsDb.Mmusculus.v79 is it fine to use this or is there any way to get the Ensdb for latest version of the genome

Thank you

ChIPpeakAnno • 354 views
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Kai Hu ▴ 20
@kai
Last seen 12 weeks ago
Worcester

The version of the annotation db must match with the genome used for mapping because the coordinates may differ for different genome releases. Therefore, if you used Mus_musculus.v103 for mapping, you'd best also use EnsDb.Mmusculus.v103 for annotation.

Below are 3 options to fetch the annotation files:

With AnnotationHub

library(AnnotationHub)

ah <- AnnotationHub()
EnsDb.Mmusculus <- query(ah, pattern = c("Mus musculus", "EnsDb"))
EnsDb.Mmusculus
EnsDb.Mmusculus.v101 <- EnsDb.Mmusculus[[length(EnsDb.Mmusculus)]]
class(EnsDb.Mmusculus.v101)

Note that AnnotationHub is not always up-to-date (it has v101 as the latest version as of 2021/03/06).

With ChIPpeakAnno::getAnnotation()

library(ChIPpeakAnno)
library(biomaRt)

listMarts()
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl")
Annotation <- getAnnotation(mart)

Note that getAnnotation() leverages biomart, which is always up-to-date.

Build your own EnsDb package (need extra effort)

There is a good tutorial on how to use makeEnsembldbPackage to generate EnsDb. It calls the Ensembl Perl API internally, and it may need some extra effort to set up the Perl environment.

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Okay Thank you for the reply I will Try above mentioned methods.

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