Mapping transcripts to mitogenome
I have performed de novo assembly of a plant mitogenome (non-model plant). In addition, I also perform de novo transcriptome assembly of this particular plant species. How to verify if the mitogenome assembly and predicted CDS is correct by making use of the RNA-Seq data?
- Should I align my sequences reads (reads) or assembled sequences (unigenes) to the mitogenome?
- What is the software recommended? MUMmer? GMAP or STAR?
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