Obtaining hg38 gene features: promoters, 5'UTR, exons, introns, 3'UTR

Question

[Sergio Martínez Cuesta]

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.

[ATpoint]

Check this out.

Answer 1

[Alex Reynolds]

Use grep or awk, e.g.:

$ awk '$3=="exon"' genes.gtf > exons.gtf

You can use BEDOPS gtf2bed to convert a GTF file to BED, and then use BEDOPS bedops and bedmap tools to calculate subsets of that BED file.

This approach can be used, for example, to get exon-intron junctions, intergenic regions, annotations that overlap SNPs with disease phenotypes of interest in promoter regions, etc. etc.