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jorainer / ensembldb

This is the ensembldb development repository.
https://jorainer.github.io/ensembldb
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I found a terrorible mistake... `genome_build: GRCh37` for v112 and `genome_build: GRCh38` for v111. #156

Closed zyh4482 closed 3 weeks ago

zyh4482 commented 3 weeks ago 
          I found a terrorible mistake... `genome_build: GRCh37` for v112 and `genome_build: GRCh38` for v111.

I understand that liftover can take care of it. But I still prefer to use GRCh38 version...

Do you have any idea how to change the annotation database to GRCh38 version?

Update: Sorry for the redundant comment. I think I found how to make it. AnnotationHub::query(ah, pattern = c("EnsDb","Homo sapiens", "GRCh38"))

> AnnotationHub::query(ah, pattern = c("EnsDb","Homo sapiens","GRCh38"))
AnnotationHub with 26 records
# snapshotDate(): 2024-04-30
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
#   tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53211"]]' 

             title                             
  AH53211  | Ensembl 87 EnsDb for Homo Sapiens 
  AH53715  | Ensembl 88 EnsDb for Homo Sapiens 
  AH56681  | Ensembl 89 EnsDb for Homo Sapiens 
  AH57757  | Ensembl 90 EnsDb for Homo Sapiens 
  AH60773  | Ensembl 91 EnsDb for Homo Sapiens 
  ...        ...                               
  AH104864 | Ensembl 107 EnsDb for Homo sapiens
  AH109336 | Ensembl 108 EnsDb for Homo sapiens
  AH109606 | Ensembl 109 EnsDb for Homo sapiens
  AH113665 | Ensembl 110 EnsDb for Homo sapiens
  AH116291 | Ensembl 111 EnsDb for Homo sapiens
> AnnotationHub::query(ah, pattern = c("EnsDb","Homo sapiens"))
AnnotationHub with 27 records
# snapshotDate(): 2024-04-30
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
#   tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53211"]]' 

             title                             
  AH53211  | Ensembl 87 EnsDb for Homo Sapiens 
  AH53715  | Ensembl 88 EnsDb for Homo Sapiens 
  AH56681  | Ensembl 89 EnsDb for Homo Sapiens 
  AH57757  | Ensembl 90 EnsDb for Homo Sapiens 
  AH60773  | Ensembl 91 EnsDb for Homo Sapiens 
  ...        ...                               
  AH109336 | Ensembl 108 EnsDb for Homo sapiens
  AH109606 | Ensembl 109 EnsDb for Homo sapiens
  AH113665 | Ensembl 110 EnsDb for Homo sapiens
  AH116291 | Ensembl 111 EnsDb for Homo sapiens
  AH116860 | Ensembl 112 EnsDb for Homo sapiens

Currently, EnsemblDB v112 is not available for GRCh38.

Maybe this will affect the output?

Originally posted by @zyh4482 in https://github.com/jorainer/ensembldb/issues/155#issuecomment-2171982790

zyh4482 commented 3 weeks ago

Sorry... I accidently click the wrong buttom...