extract gene/transcript sequence from ttophat/cufflink/cuffdiff output

[mehtaaditya]

Hi every one
i work on RNA seq data. i used Tophat/cufflink pipeline to study referenced based RNA seq data analysis. after run all the step tophat, cufflink, and last cuffdiff for differential gene expression study i stuked at one place in my study. i want to extract differentially expressed gene/transcript sequence. but i dont know how can i extract gene/transcript sequence from my output files. i also have my reference genome file.how can i obtained this sequences can anybody help me to solve this problem? Thanks in advance.

[sindrle]

For reference sequences, look at bottom of the page:

http://cufflinks.cbcb.umd.edu/gff.html

For novel sequence, I don't know..

[mehtaaditya]

Thanks....