I have done a de novo transcriptome assembly and annotation for a non-model plant. For generating a robust assembly, the equal amount of total RNA extracted from various tissue were mixed to make one pool for sequencing. Then, I calculated FPKM value for this assembly, interestingly some of the genes of interest got the high FPKM value, which encourages me to validate their presence via qRT-PCR. Now, my question is: considering the assembly was made from various tissues if selecting genes based on FPKM value to validate the assembly accuracy is reasonable?
Thank you for all your comments and suggestion in advance