splice junction file for human(hg19)

Question

[Govardhan Anande]

Where can I get splice junction annotation file for human(hg19), in order to run tophat with --raw-juncs.

Thanks in advance

[cfarmeri]

In tophat manual, when "you supply your own transcript annotation data", you should use "--raw-juncs." option.

Normaly(i.e. when dont have our OWN transcript annotation data including splice junction interval), GFF or GTF annotation file includes splice junction informatin.