Hi all,
Sorry ahead of time, RNA-Seq and bioinformatics is something I am new at and still learning as I go. I am trying to compare the sequences of a single gene across different species using RNA-Seq data to identify (structural) variants or anything mutations in different species that may impact function. Thankfully there is already a reference CDS of the gene, on NCBI, that I am focusing on.
The issue I am encountering is that I do not know of the proper workflow or methodology to compare this one gene across multiple species. Ultimately I may be, and probably am, overthinking and overcomplicating the process. Is it as simple as using BLAST with the gene or my RNA-Seq data as a reference? Any advice or suggestions would be much appreciated.
Thank you!
Never mind my plan going forward is to use mafft (through OrthoFinder) by adding the fasta of my gene of interest to my samples and then searching for it manually