Is there a way to run Cufflinks' cuffcompare in a strand-agnostic mode?

I would like to do this because I have some RNA-seq datasets derived from an unstranded run, that should be compared to a reference transcriptome. I think that it makes no reason to have some transcripts in the experimental dataset classified with transfrag code tag x and s as compared to the reference if the input dataset was not derived from stranded protocol.

From manual:

x : Exonic overlap with reference on the opposite strand

s : An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)

Conceptually, does it make sense?

If so, and if the run by cuffcompare cannot be changed to a strand-agnostic manner, how should I interprete those transcripts classified as x? I was thinking of merging them to o and/or c .

Again, from manual:

c : Contained

o : Generic exonic overlap with a reference transcript



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