Hello!
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?
Greetings
For de novo assembly, if not already completed, try Trinity.
Then you can use the tool transdecoder on your contigs to predict ORFs and get protein seqs etc.