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News: Ensembl release 81 is out!
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gravatar for Thomas Maurel
2.4 years ago by
Thomas Maurel700
United Kingdom
Thomas Maurel700 wrote:

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 

ADD COMMENTlink modified 2.4 years ago by Sonali Arora360 • written 2.4 years ago by Thomas Maurel700
2
gravatar for Sonali Arora
2.4 years ago by
Sonali Arora360
United States
Sonali Arora360 wrote:

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. 

 

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Sonali Arora360

Thanks Sonali!

Alternatively you can create an EnsDb database using ensembldb

> library(ensembldb)
> db <- ensDbFromGRanges(gr, organism="Homo_sapiens", version=81, genomeVersion="GRCh38")
> edb <- EnsDb(db)

> edb
EnsDb for Ensembl:
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.0.1
|Creation time: Sat Jul 18 21:41:07 2015
|ensembl_version: 81
|ensembl_host: unknown
|Organism: Homo_sapiens
|genome_build: GRCh38
|DBSCHEMAVERSION: 1.0
|source_file: GRanges object
| No. of genes: 65988.
| No. of transcripts: 216133.

> seqinfo(edb)
Seqinfo object with 331 sequences from GRCh38 genome:
  seqnames           seqlengths isCircular genome
  1                   248956422       <NA> GRCh38
  2                   242193529       <NA> GRCh38
  3                   198295559       <NA> GRCh38
  4                   190214555       <NA> GRCh38
  5                   181538259       <NA> GRCh38
  ...                       ...        ...    ...
  KI270723.1              38115       <NA> GRCh38
  CHR_HSCHR13_1_CTG5  114365350       <NA> GRCh38
  KI270707.1              32032       <NA> GRCh38
  KI270752.1              27745       <NA> GRCh38
  MT                      16569       <NA> GRCh38

 

cheers, jo

ADD REPLYlink written 2.4 years ago by Johannes Rainer1.1k
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