News:EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
0
3
Entering edit mode
Johannes Rainer ★ 1.9k
@johannes-rainer-6987
Last seen 5 hours ago
Italy

Dear all,

I've added ensembldb EnsDb databases for all species of Ensembl release 98 to AnnotationHub. These databases provide now also the G-C nucleotide content for each transcript in metadata column "gc_content" (see below).

cheers, jo

> library(AnnotationHub)
> query(AnnotationHub(), "EnsDb", "v98")
snapshotDate(): 2019-10-29
AnnotationHub with 1321 records
# snapshotDate(): 2019-10-29 
# $dataprovider: Ensembl
# $species: Homo sapiens, Ailuropoda melanoleuca, Anolis carolinensis, Astya...
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53185"]]' 

            title                                      
  AH53185 | Ensembl 87 EnsDb for Anolis Carolinensis   
  AH53186 | Ensembl 87 EnsDb for Ailuropoda Melanoleuca
  ...       ...                                        
  AH75116 | Ensembl 98 EnsDb for Xenopus tropicalis    
  AH75117 | Ensembl 98 EnsDb for Zonotrichia albicollis
> edb <- AnnotationHub()[["AH75117"]]
snapshotDate(): 2019-10-29
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
require(“ensembldb”)
> transcripts(edb)
GRanges object with 30624 ranges and 9 metadata columns:
                           seqnames       ranges strand |              tx_id
                              <Rle>    <IRanges>  <Rle> |        <character>
  ENSZALT00000030003 ARWJ01023036.1 21700-155713      + | ENSZALT00000030003
  ENSZALT00000030004 ARWJ01023036.1 21700-155713      + | ENSZALT00000030004
                 ...            ...          ...    ... .                ...
  ENSZALT00000002807     KB915622.1  13173-14579      - | ENSZALT00000002807
  ENSZALT00000002808     KB915622.1  13173-14579      - | ENSZALT00000002808
                         tx_biotype tx_cds_seq_start tx_cds_seq_end
                        <character>        <integer>      <integer>
  ENSZALT00000030003 protein_coding            21700         155677
  ENSZALT00000030004 protein_coding            21700         155207
                 ...            ...              ...            ...
  ENSZALT00000002807         lncRNA             <NA>           <NA>
  ENSZALT00000002808         lncRNA             <NA>           <NA>
                                gene_id tx_support_level        tx_id_version
                            <character>        <integer>          <character>
  ENSZALT00000030003 ENSZALG00000017908             <NA> ENSZALT00000030003.1
  ENSZALT00000030004 ENSZALG00000017908             <NA> ENSZALT00000030004.1
                 ...                ...              ...                  ...
  ENSZALT00000002807 ENSZALG00000001837             <NA> ENSZALT00000002807.1
  ENSZALT00000002808 ENSZALG00000001837             <NA> ENSZALT00000002808.1
                           gc_content            tx_name
                            <numeric>        <character>
  ENSZALT00000030003  42.803825519011 ENSZALT00000030003
  ENSZALT00000030004 42.7888065056207 ENSZALT00000030004
                 ...              ...                ...
  ENSZALT00000002807 51.9956850053937 ENSZALT00000002807
  ENSZALT00000002808 52.7659574468085 ENSZALT00000002808
  -------
  seqinfo: 1729 sequences from Zonotrichia_albicollis-1.0.1 genome

annotation ensembldb EnsDb AnnotationHub News • 296 views
ADD COMMENT

Login before adding your answer.

Traffic: 376 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6