having problem with cufflinks output

Question

[hana]

Hi

I have run tophat with --GTF option and also run cufflinks with --GTF option too. The 7 cloumn of transcript.gtf file should be '+', '-' or '.', however I got 0 for all genes in 7 cloumn. I am wondering if anybody met the same problem before?

thank you

[Devon Ryan]

Are you sure you're looking at the correct column (and not column 8)? Can you post a few lines of the file?