Is transcript color accessible through ensembldb? (gold = in both HAVANA+ENSEMBL)
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Aditya ▴ 160
@aditya-7667
Last seen 22 months ago
Germany

Is Ensembl transcript color available through ensembldb?

I especially want to know whether it is gold colored: i.e. in both HAVANA as well as ENSEMBL

E.g. IQCC-202.

ensembldb • 768 views
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Johannes Rainer ★ 2.0k
@johannes-rainer-6987
Last seen 22 days ago
Italy

No, color information or whether a transcript is both in HAVANA and ENSEMBL is not provided by ensembldb EnsDb databases. You can however get transcript support level (TSL) for each transcript in column "tx_support_level":

> library(AnnotationHub)
> library(ensembldb)
> ah <- AnnotationHub()
snapshotDate(): 2020-06-18
> query(ah, "EnsDb.Hsapiens.v96")
AnnotationHub with 1 record
# snapshotDate(): 2020-06-18
# names(): AH69187
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# $rdatadateadded: 2019-04-15
# $title: Ensembl 96 EnsDb for Homo sapiens
# $description: Gene and protein annotations for Homo sapiens based on Ensem...
# $taxonomyid: 9606
# $genome: GRCh38
# $sourcetype: ensembl
# $sourceurl: http://www.ensembl.org
# $sourcesize: NA
# $tags: c("96", "AHEnsDbs", "Annotation", "EnsDb", "Ensembl", "Gene",
#   "Protein", "Transcript") 
# retrieve record with 'object[["AH69187"]]' 
> edb <- ah[["AH69187"]]
loading from cache
> transcripts(edb)
GRanges object with 230399 ranges and 8 metadata columns:
                  seqnames            ranges strand |           tx_id
                     <Rle>         <IRanges>  <Rle> |     <character>
  ENST00000456328        1       11869-14409      + | ENST00000456328
  ENST00000450305        1       12010-13670      + | ENST00000450305
              ...      ...               ...    ... .             ...
  ENST00000435741        Y 26626520-26627159      - | ENST00000435741
  ENST00000431853        Y 56855244-56855488      + | ENST00000431853
                              tx_biotype tx_cds_seq_start tx_cds_seq_end
                             <character>        <integer>      <integer>
  ENST00000456328   processed_transcript             <NA>           <NA>
  ENST00000450305 transcribed_unproces..             <NA>           <NA>
              ...                    ...              ...            ...
  ENST00000435741   processed_pseudogene             <NA>           <NA>
  ENST00000431853   processed_pseudogene             <NA>           <NA>
                          gene_id tx_support_level     tx_id_version
                      <character>        <integer>       <character>
  ENST00000456328 ENSG00000223972                1 ENST00000456328.2
  ENST00000450305 ENSG00000223972             <NA> ENST00000450305.2
              ...             ...              ...               ...
  ENST00000435741 ENSG00000231514             <NA> ENST00000435741.1
  ENST00000431853 ENSG00000235857             <NA> ENST00000431853.1
                          tx_name
                      <character>
  ENST00000456328 ENST00000456328
  ENST00000450305 ENST00000450305
              ...             ...
  ENST00000435741 ENST00000435741
  ENST00000431853 ENST00000431853
  -------
  seqinfo: 423 sequences from GRCh38 genome

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