Recently I worked on assembling a transcriptome of a non-model organism. I was told the RNA-seq data was not strand-specific, and I assembled the transcriptome with Trinity, using the not strand-specific option.
It turns out that the reads are actually strand-specific. I would like to know what are the consequences of keeping the current transcriptome (in other words, of analyzing strand-specific data as not strand-specific).
My study organism is a vertebrate, so I don't think the genome is particularly compact. The main use of this transcriptome was to guide a genome annotation process. We are quite satisfied with the annotation derived from the current transcriptome.
I know that the best thing to do would be to redo the analyses, but this would be time consuming and would require a lot of computing resources, that we don't have right now. I guess I am looking for reasons to convince my boss that this is what we should do.