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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:
- 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. - When I use the
featureCounts
ofSubread
package (v2.0.3, command-line version), will-g gene_id -t transcript
and-g gene_id -t gene
give me same results?