I'm doing a de novo assembly with reads obtained with Stranded type illumina sequencing. I guess it's Stranded Forward since the Read 1 map with the cDNA antisense and the Read 2 with the cDNA sense (and therefore they are in the opposite direction, Read 1 sense, Read 2 antisense). However, after doing the assembly de novo, I translate the transcripts obtained and the proteins present a negative frame. Wouldn't it be expected that all of them would have a positive frame since it is a stranded-forward protocol, where the reads sense would be taken as reference? Or am I getting confused and is it really a reverse protocol?