Cuffcompare Output '-' Versus Fpkm = 0

Question

[User 4409]

The Cufflinks manual states that in the 6th column of the Cuffcompare *.tracking output:

A sample not containing a transcript will have a "-" in its entry in the row for that transcript.

This is the column containing this information:

qJ:geneid|transcriptid|FMI|FPKM|conflo|confhi|cov|len

So... What's the difference between an entry of '-' versus q1:CUFF.21|ACYPI065857-RA|0|0.000000|0.000000|0.000000|0.000000|408?

[pengchy]

This problem still exists now, although cufflinks has been updated many times.