Hi guys,
I'm doing a strand specific RNA-seq with dUTP incorporation during the second strand synthesis of cDNA and posterior UDgase treatment. after the mapping of the reads using tophat I get the reads in an opposite orientation of the gene (see attachment). Since I'm sequencing only the first strand I suppose the I would get the tags in the same direction of the genes is that correct? so, could this inversion be cause by the mapping with tophat?
thanks for your comments!
I'm doing a strand specific RNA-seq with dUTP incorporation during the second strand synthesis of cDNA and posterior UDgase treatment. after the mapping of the reads using tophat I get the reads in an opposite orientation of the gene (see attachment). Since I'm sequencing only the first strand I suppose the I would get the tags in the same direction of the genes is that correct? so, could this inversion be cause by the mapping with tophat?
thanks for your comments!