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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.