Cufflinks - LOWDATA and NOTEST in *.diff files

[szaks]

After running cuffdiff, in all of the *.diff files the test status is “LOWDATA”, “NOTEST”, or, to a smaller extent, “FAIL.” On the other hand, the *_exp.diff files are fine; many of the test status are "OK". Any thoughts why this might be happening?

The LOWDATA status is strange, as all of my targeted genes have >1000x coverage. Of note, this is targeted RNASeq data set; we only sequenced 30 genes. Maybe the targeted nature of the data set is the problem? The .gtf file that I'm using has all human genes in it; should I parse out our targeted genes of interest and use the smaller gtf file?

I'm using cufflinks v2.0.2.

Thanks in advance for any advice, guidance, or direction!

[ramiro2k]

Any answers?

Did you find a solution to this?? I am experiencing the same problem...