cuffdiff generates empty files

[potato84]

Hi all,

I used cuffdiff to compare samples. I didn't use any special options, but it generates empty files. Those files even don't have the title line. Does anybody have similar experience? or know what happened?

It worked for some of my data. In the result folder, the gene_exp.diff looks like right. Although other files, promoters.diff,cds.diff,etc., are empty with the title line.

Thanks!

[blanco]

Hi,
I have a similar problem. I ran cuffdiff and all output files seem ok except the cds ones, which are empty.

I ran cuffdiff with the -u option for the merged .gtf file from cuffmerge as well as with the -b option for the reference genome.

It would be nice to have some explanation for this.