By convention, i understand that when a mRNA sequence is obtained, it is automatically formatted as cDNA for computational analysis. (the U nucleotide is automatically formatted as T)
I am having trouble finding publications which illustrate mRNA sequence analysis in text or in figures showing convention in practice - showing an mRNA sequence illustrated in cDNA format or simply in AGTC versus AGUC format.
MAIN POINT: I have transcriptome data, and I'm outlining some SNPs within a single transcript. By convention, this transcript should be presented as cDNA. I would like to see some publications who have done this or something similar, literally writing out their mRNA sequence using DNA nucleotides. Anyone know any such articles so I can see it within a publication?
I have only been able to find one article so far which illustrates this: https://www.sciencedirect.com/science/article/pii/S0888754313000682
Thank you for clarifying this! I am very grateful.