How to convert transcript-relative coordinates to genomic coordinates?
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4 months ago

I have queried using Entrez Utilities (efetch: https://www.ncbi.nlm.nih.gov/books/NBK25499/) and obtained annotations for transcripts like the following:

>Feature ref|NM_152486.3|

1 2557 gene

        gene    SAMD11

gene_syn    MRS

gene_desc   sterile alpha motif domain containing 11

db_xref GeneID:148398

db_xref HGNC:HGNC:28706

db_xref MIM:616765


How/what database should I query to get the proper genomic coordinates for this gene and convert the transcript coordinates to absolute genomic coordinates?

IMPORTANT!: many of these transcripts are out of date, so just getting a table from UCSC is out of the question (unless transcript ID doesn't matter for getting genomic coordinates...)

Thanks!

refseq transcript • 239 views
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You will need to find the annotation release when the RefSeq was last annotated and extract that information from the GFF3/GTF files for that annotation. Since this is a human gene, which version of the genome are you interested: GRCh38/hg38 or GRCh37/hg19?