Hi everyone, I have recently assembly a draft genome. I consider it has an acceptable quality based on the assessment I made and my biological goals. Before I have the genome assembly ready, I performed a de novo transcriptome assembly of this species and, after some analysis, I found some candidate genes to be duplicated in the genome. My idea to check this by mapping the reads to these transcripts (candidates) and to the genome and the check the positions of those reads that have mapped both. I am a beginner in this area, so I would like to know your ideas and advice about it.
Thanks in advance.