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News: ensembl 87 and 88 gtfs and fasta twobits have been added to AnnotationHub
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4 months ago by
shepherl ♦♦ 380
shepherl ♦♦ 380 wrote:

Hello all, 

The ensembl 87 and 88 gtfs (converted to GRanges on the fly) have been added to AnnotationHub and are currently available:

> library(AnnotationHub)

> hub = AnnotationHub()
updating metadata: retrieving 1 resource

|======================================================================|
100%
snapshotDate(): 2017-04-04

> length(query(hub, c("ensembl", "gtf", "release-87")))
[1] 218
> length(query(hub, c("ensembl", "gtf", "release-88")))
[1] 218

 

The fasta (twobit files) for release-87 and release-88 have been added to AnnotationHub and are currently available in Bioc3.6 (development) with AnnotationHub (<= 2.9.0): 

 

> library(AnnotationHub)
> hub = AnnotationHub()
updating metadata: retrieving 1 resource

|======================================================================|
100%
snapshotDate(): 2017-04-26

> length(query(hub, c("fasta", "release-87", "twobit")))
[1] 425

> length(query(hub, c("fasta", "release-88", "twobit")))
[1] 425

 

Thank you

ADD COMMENTlink modified 4 months ago • written 4 months ago by shepherl ♦♦ 380
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