Hello, I planned to explore diverse T cell receptor transcripts using long-read sequencing. So I transfected TCR mini gene into cells and got sequencing data.
I mapped my data to genome reference and visualize it via IGV. But I couldn't see any transcripts from TCR plasmid on the chromosome 7 where T cell receptor locus is.
How can I detect reads from transfected plasmid? Shall I make custom reference file using plasmid map?
Or should I use any specific ways to detect TCR transcripts like IGMT, MiXCR, IgBLAST and so on?
I just want to see the diversity of splicing patterns using tools like FLAIR.
I need your advice! Thank you.