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Question: Detection T cell receptor transcripts
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gravatar for jsw940
7 months ago by
jsw940 • 10
jsw940 • 10 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 • 199 views
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modified 6 months ago by caggtaagtat • 1.4k • written 7 months ago by jsw940 • 10
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gravatar for caggtaagtat
6 months ago by
caggtaagtat • 1.4k
caggtaagtat • 1.4k 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 COMMENT • link written 6 months ago by caggtaagtat • 1.4k
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