I'm trying to use TopHat and Cufflinks mainly for differential gene expression analysis according to the protocol by Trapnell et al. (Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks). I use strand-specific SOLiD reads (paired end) with the option --library-type fr-secondstrand.
My question: In the manual it is mentioned that TopHat and Cufflinks are strand aware, does this mean that only reads which are from the sense strand of the gene/transcript are taken into account for FPKM calculation?
If yes, is there also an option to use both or only antisense reads (something similar to htseq-count's stranded option)?
My question: In the manual it is mentioned that TopHat and Cufflinks are strand aware, does this mean that only reads which are from the sense strand of the gene/transcript are taken into account for FPKM calculation?
If yes, is there also an option to use both or only antisense reads (something similar to htseq-count's stranded option)?