Question: Detection T cell receptor transcripts
gravatar for jsw940
8 weeks ago by
jsw94010 wrote:

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.

rna-seq next-gen sequence • 131 views
ADD COMMENTlink modified 29 days ago by caggtaagtat1.3k • written 8 weeks ago by jsw94010
gravatar for caggtaagtat
29 days ago by
caggtaagtat1.3k wrote:

Hi, as you said, you could add the sequence of your minigene to your reference fasta. After uploading it to IGV, there will be a new option in the chromosome select field to view reads mapping on the mini-gene.

Maybe you have artificial subsequences in your minigene, which makes it different from the original locus.

ADD COMMENTlink written 29 days ago by caggtaagtat1.3k
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