Strand-specific Expression analysis in Cufflinks
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)?