Relationship between gene_id and transcript_id genomic coordinates
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@8f57c5c1
Last seen 8 months ago
United States

I am confused about the genomic coordinates of a "gene" entry in a GTF file. For example, the human gene PRDM2 (ENSG00000116731) has 14 transcripts according to Ensembl, and the coordinates of the gene entry is Chromosome 1: 13,700,188-13,825,079. Then I have two questions:

  1. Is the genomic coordinates of the gene PRDM2 equal to merge of all the 14 transcript variants? Here "merge" means combining overlapping transcripts into a single feature, just like what bedtools merge does.
  2. When I use the featureCounts of Subread package (v2.0.3, command-line version), will -g gene_id -t transcript and -g gene_id -t gene give me same results?
Rsubread ensembldb • 478 views
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@james-w-macdonald-5106
Last seen 18 hours ago
United States

This support site is meant to help people with questions about Bioconductor tools. Your first question is a basic biology/annotation question, and the second pertains to a non-Bioconductor package. You might consider asking over at biostars.org instead.

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