We are for the first time mapping stranded RNA-seq paired reads sequenced with the Illumina TruSeq protocol. We are using TopHat2 with the fr-firststrand option and we notice that the direction of reads on the genome seems to depend on the order of the read pair files inputted for mapping. And this will also affect the gene counts later on. It looks that setting R2 reads before R1 gives the correct results. But I can't seem to find this in the TopHat manual.
Are there any standard ways of mapping paired-end stranded RNA-seq reads?