Entering edit mode
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.
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.
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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