Dear all, I have several RNAseq paired end datasets that I want to pool for input into a Trinity de novo assembly. The problem is that half of my datasets are of library type RF (first read (/1) of fragment pair is sequenced as anti-sense (reverse(R)), and second read (/2) is in the sense strand (forward(F))) and half of my data are FR: first read (/1) of fragment pair is sequenced as sense (forward), and second read (/2) is in the antisense strand (reverse).
Is there a way to convert the library type? Simply reverse complementing the reads will not work since then they won't be "pointing" at each other. Any ideas?