Which approach do you find useful to extract gene features (promoters, 5'UTR, exons, introns, 3'UTR ) from the annotation file (genes.gtf) of a reference genome e.g. the iGenomes UCSC hg38?
I often use the functions available in the GenomicFeatures bioconductor package, e.g. makeTxDbFromGFF, promoters, genes, transcripts, ...
library(GenomicFeatures) txdb <- makeTxDbFromGFF("genes.gtf", format="gtf") promoters(txdb) # extracting promoters exons(txdb) # extracting exons
However I was wondering which other strategies are commonly used in general when genes features are needed. Any ideas would be helpful.