using gmap to find tss and tes in genome file.

Question

[a.rex]

I wish to annotate my genome of interest with TES's and TSS's. Is the best way to do this to use gmap to map my transcriptome to the genome? What sort of output can I expect from gmap and can I parse this easily to get the TSS's and TES's?

[WouterDeCoster]

It's unclear which data you have for mapping using gmap. Gmap can give you a sam file output, optionally junction files and perhaps more specific output with regard to your analysis, but for that I would suggest you to Read The Fantastic Manual.