Request for Guidance on RNA Transcriptomic Analysis?

07 December 2024 0 3K Report

Dear Experts,

I hope this message finds you well. I would greatly appreciate your assistance. I am currently pursuing my PhD and working on RNA transcriptomic analysis using PacBio data. I have obtained all mitochondrial transcripts (Iso-seq) from the transcriptome data and compared them to the reference mitochondrial genome using BLAST and minimap2 software. After sorting the transcripts by alignment length, I have the following questions:

How can I determine the primary transcripts (3' end?), intermediate transcripts, and mature transcripts (mitochondrial rRNA, tRNA, and mRNA)? If I select the top 3 transcripts based on alignment length, would they be considered primary transcripts? If so, what about the intermediate and mature transcripts?

How can I infer the boundaries of mitochondrial RNA (mtRNA) genes and identify the start and stop codon types for protein-coding genes from mature transcripts?

I would greatly appreciate your guidance on these points as I am a bit confused.

Thank you in advance for your time and assistance. I look forward to your response.

Best regards,

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