how I can extract needed gene list (txt) from a bed file

Question

[zizigolu]

Hi,

I have three bed files (insertion, deletion and junction) in my tophat out put. I need to extract the genes as txt file by biophyconnector package. Then which bed file I should use as input?

Thanks

[LauferVA]

could you provide a little snippet of each please

[zizigolu]

Actually me myself also don know enough about the details just I know I want to divide the average number of reads per length of mrna from riboseq on the average number of reads from the rnaseq...I did rnaseq with tophat and in output I have such a file but for boiphysconnector I need sam files to be converted to the txt file each on for riboseq and rnaseq and a bed file for riboseq also I need but I donno which riboseq bed from tophat output I should use