I have completed the task of comparing mitochondrial transcripts to the reference mitochondrial genome, sorting the transcripts by length. Now, I would like to focus on two further steps:
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Determine the primary transcripts (e.g., the pre-mRNA), intermediate transcripts, and mature transcripts (mitochondrial rRNA, tRNA, and mRNA).
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What are the best methods or tools to classify and differentiate these types of transcripts from mitochondrial RNA (mtRNA)? Are there specific features in the sequencing data that help identify primary, intermediate, and mature transcripts
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Infer the boundaries of mitochondrial RNA (mtRNA) genes and the start and stop codon types of protein-coding genes from the mature transcripts
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How can I accurately determine the boundaries of mitochondrial genes (rRNA, tRNA, and mRNA) from my transcript data? What tools or strategies can be used to infer the start and stop codons for protein-coding genes? Any resources, tools, or approaches you can recommend for completing these tasks would be greatly appreciated!
