Does anyone know how cufflinks counts stranded data?

[JonB]

Hi,

I'm trying to make sense of the fpkm/coverage values produced by cufflinks. I have mapped paired-end stranded illumina data (fr-firststrand type).

But the coverage values are not similar to the ones produced by HTSeq, and I can't see that cufflinks takes into account the strandedness (because I tried to map with different order of input reads, i.e. both R1 R2, or R2 R1, and I get coverage both times. And with HTSeq I only get coverage for one of the orders)