Is it possible to output ensembl id for annotatr build_annotations basicgenes?
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Ahdee ▴ 50
@ahdee-8938
Last seen 9 weeks ago
United States

I'm using the annotatr package and notice the build_annotations function gives different tx_id depending on whether its from hg19 or hg38. for example

build_annotations(genome = 'hg38', "hg38_basicgenes"  )
build_annotations(genome = 'hg19', "hg19_basicgenes"  )

hg38 looks like this.

Ranges object with 3551273 ranges and 5 metadata columns:
                    seqnames        ranges strand |          id             tx_id     gene_id       symbol                 type
                       <Rle>     <IRanges>  <Rle> | <character>       <character> <character>  <character>          <character>
        [1]             chr1   10869-11868      + |  promoter:1 ENST00000456328.2   100287102      DDX11L1 hg38_genes_promoters
        [2]             chr1   11010-12009      + |  promoter:2 ENST00000450305.2   100287102      DDX11L1 hg38_genes_promoters
        [3]             chr1   28554-29553      + |  promoter:3 ENST00000473358.1        <NA>         <NA> hg38_genes_promoters

where as hg19 looks like this.

GRanges object with 1746407 ranges and 5 metadata columns:
                  seqnames        ranges strand |          id       tx_id     gene_id      symbol                 type
                     <Rle>     <IRanges>  <Rle> | <character> <character> <character> <character>          <character>
        [1]           chr1   10874-11873      + |  promoter:1  uc001aaa.3   100287102     DDX11L1 hg19_genes_promoters
        [2]           chr1   10874-11873      + |  promoter:2  uc010nxq.1   100287102     DDX11L1 hg19_genes_promoters
        [3]           chr1   10874-11873      + |  promoter:3  uc010nxr.1   100287102     DDX11L1 hg19_genes_promoters
        [4]           chr1   68091-69090      + |  promoter:4  uc001aal.1       79501       OR4F5 hg19_genes_promoters
        [5]           chr1 320084-321083      + |  promoter:5  uc001aaq.2        <NA>        <NA> hg19_genes_promoters
        ...            ...           ...    ... .         ...         ...         ...         ...                  ...
  [1746403] chrUn_gl000228 107268-107275      + |  3UTR:64358  uc031tgq.1       22947      DUX4L1     hg19_genes_3UTRs
  [1746404] chrUn_gl000228 110574-110581      + |  3UTR:64359  uc031tgr.1       22947      DUX4L1     hg19_genes_3UTRs
  [1746405] chrUn_gl000228 113880-113887      + |  3UTR:64360  uc031tgs.1      728410      DUX4L2     hg19_genes_3UTRs
  [1746406] chrUn_gl000228   29339-30529      - |  3UTR:64361  uc011mgh.2   100288255        <NA>     hg19_genes_3UTRs

is there anyway to get hg19 version to use ensembl id instead?

thanks.

Annotation annotatr • 132 views
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