tophat->cufflinks->cuffdiff library type

[nlign]

Hi folks,

I am doing RNA-seq analysis using tophat->cufflink->duffdiff pipeline on a stranded dataset.

I ran tophat2 with "--library-type ff-firststrand" but in the subsequent run of cufflinks and cuffquant I did not use "--library-type ff-firststrand" . Does that affect my results in any way?

Thanks you all in advance
naren