annotated deltions

[paolo.kunder]

Dear All,
I would like to load in IGV my Tophat reported deletions and a database of human annotated deletions, where I do find the latter one?

Thanks,
Paolo

[giuliano stirparo]

I have a similar problem. Where can I find the human junction annotation (.bed format that should be converted in .juncs format) to supply tophat alignment.
Thanks
Giulio

[Orr Shomroni]

Where you get your BED file depends on which kit you are working with. When working with Nimblegen/Roche kit, you can download it from the Internet. If you are working with Agilent, you need to ask them for a CD with the newest version, because I don't think it is on the web (at least I couldn't find it). About other kits, I don't know.
I hope you know how to convert the .bed to .juncs files, or how to show TopHat alignments in IGV, because I don't know how to do either :-P