I assembled a transcriptome using Trinity with setting of --SS_lib_type R, then I continued to predict ORFs using TransDecoder. The final result gives me 236711 ORFs with 202113 on + strand of transcripts. This is a good sign to show strand-specific setting worked. but I am not sure whether I should retain those ~ 20000 ORFs predicted on - strand.
I will further do DE analysis and SNP calling. Will retaining those minus-strand ORF affect my following analysis?