gene name in cufdiif output?

[semna]

Hi
I use the new version of cufflinks and I run simple cufflinks, then run cuffcompare with -r and finally run cuffdiff with -N and used combined gtf. but I don't have any gene name in my output? Thanks for your help in advance.
reza

[Mark Admr]

Hi,
i don't know about it but i think you will get your desired help by searching social network.
You can try.

[junshen]

Did you use a .gtf file?

[semna]

yes, for cuffcompare used gtf file from ensembl and in cuffdiff used stdout.combined.gtf and two bam files.