Is third-generation sequencing/long-read-sequencing the only way to identify the full length sequence of a novel transcript?

Is third-generation sequencing/long-read-sequencing the only way to identify the full length sequence of a novel transcript?

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Thanks for your attention,

TLDR:
How to get the full length sequence of a novel transcript?

Details:

  1. There is a novel transcript A I identified using short-read sequencing, through assembly. It contains an unique sequence I have validate using PCR, I refer to it as ATCGATCG for illustration.
  2. Because In-silico assembly using short, pair-end read is quite noisy. I want to clearly know the full length sequence of the transcript A, which is XXXXATCGATCGXXXXXXXX where X indicate bases I didn’t know.
  3. I know that 3rd generation sequencing could get full length transcript. However, it’s expensive. And I’m not interested in every transcript, transcript A.
  4. So, Is there any cost-effective way to get the full length sequence?

Any clue or guidance is highly appreciated!


long-read-sequencing


third-generation-sequencing


transcript

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