Hi, I'm interested in analyzing average density of reads from CLIP-seq experiments in the 3'UTR and around TES (transcription end site) of genes. For ChIP-seq analysis, the promoters function of "GenomicFeatures" package computes a GRanges object that spans the promoter region around the transcription start site for the transcripts in a TxDb object.Subsequent upstream 0and downstream arguments define the number of bases upstream and downstream from the transcription start site that make up the promoter region. How to create a GRanges object that spans region around TES (transcription end site) of the genes? Thank you, Marco

I guess you could invert the strand and use promoters(). Another option is flank(gr, width, both=TRUE, start=FALSE) but note that the width is divided equally upstream and downstream (it's symmetric).