Alternative first exon annotation database

Question

[maximus3219]

I would like to find out any changes in alternative first exon usage (as surrogate marker for promoter usage) in diffrent genes between cancer and normal samples.

There is .bed file and .txt annotation file from FANTOM5 CAGE project, indicating the location of each transcription start sites (TSS).

I am wondering how I can create a annotation or database files indicating all the alternative first exon of each genes, so that I can calculate the coverage of each alternative first exon to determine any differential usage of alternative first exons.

How do I utilized the data from CAGE? Or any other methods I can achieve my goal?

Thanks!

[Kristoffer Vitting-Seerup]

Could you be a bit more specific - seems like you are asking 3 different things. What are you actually interested in getting help with?

[maximus3219]

I mean can I use the .bed file and .txt annotation file from FANTOM5 to determine the location of TSS/first exon, and then to determine any differential usage of TSS/first exon. Any software/program that allows me to do this?