Dear all,

We are pleased to announce that the new Ensembl marts for release 81 are now live on www.ensembl.org.

If you are using biomaRt, you can change your host to access our most recent data (With R 2.2 and Bioconductor version 3.1):

ensembl_mart_81 <- useEnsembl(biomart=“ensembl")

• Ensembl Genes 81
  • Human assembly updated from GRCh38.p2 to GRCh38.p3
  • Mouse assembly updated from GRCm38.p3 to GRCm38.p4
• Ensembl Variation 81
  • Human assembly updated from GRCh38.p2 to GRCh38.p3
  • Mouse assembly updated from GRCm38.p3 to GRCm38.p4    
  • Added new structural variation species Sheep (Ovis aries)
• Ensembl Regulation 81
  • New mouse regulation build data
• Vega 61
  • Human assembly updated from GRCh38.p2 to GRCh38.p3
  • Mouse assembly updated from GRCm38.p3 to GRCm38.p4

A complete list of the changes in release 81 can be found at http://www.ensembl.org/info/website/news.html

Best Regards,

Thomas 

We have added the GTF files from Ensembl's release-81 to Bioconductor (Bioc version 3.1 and 3.2). You can access them via AnnotationHub: 

> library(AnnotationHub)
> ah = AnnotationHub()
snapshotDate(): 2015-07-17

> gtf_hs_81 <- query(ah, c("ensembl","gtf", "81", "homo sapiens"))

> gtf_hs_81 # access data about the file
AnnotationHub with 1 record
# snapshotDate(): 2015-07-17
# names(): AH47963
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: GRanges
# $title: Homo_sapiens.GRCh38.81.gtf
# $description: Gene Annotation for Homo sapiens
# $taxonomyid: 9606
# $genome: GRCh38
# $sourcetype: GTF
# $sourceurl: ftp://ftp.ensembl.org/pub/release-81/gtf/homo_sapiens/Homo_sap...
# $sourcelastmodifieddate: 2015-07-07
# $sourcesize: 49757610
# $tags: GTF, ensembl, Gene, Transcript, Annotation
# retrieve record with 'object[["AH47963"]]'

> gr <- gtf_hs_81[["AH47963"]]   # download the file as an GRanges object.

Optionally, create a transcript data base using GenomicFeatures

> txdb <- GenomicFeatures::makeTxDbFromGRanges(gr)
> txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Genome: GRCh38
# transcript_nrow: 216133
# exon_nrow: 733504
# cds_nrow: 293948
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-07-17 12:23:57 -0700 (Fri, 17 Jul 2015)
# GenomicFeatures version at creation time: 1.21.13
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1

Best,

Sonali.