Blank gene_id and gene rows

[kasutubh]

Hello everyone,

So this is how it goes..I run cuffdiff and end up with all the output files. Only the files with the isoform heading give data..while all the others (genes,tsp,cds) are blank. Also in the isoform_exp.diff file, the gene_id and gene rows are blank. The file does generate the FPKM values across conditions. What might be the reason for this? Is this the problem with the .gff file I'm using as a reference?

Thanks in advance!