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Fusion sequence matching

Hello everyone, I was wondering if it would make any sense to detect gene fusions in my RNA seq data by just matching the sequence around the fusion point to my reads. What do you think?

Thank you and happy holidays! :)

Peny

rna-seq fusions gene fusions
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written by pennakiza pennakiza

2 answers

Hello Peny, great to see you on Christmas Eve/Day,

The description of your idea is too vague, and I am not going to enter a 'back and forth' discussion on what you mean, exactly. So, perhaps you should just confirm your hypothesis by looking at a few or all of the [shocking number of] fusion gene detection programs that are out there: A: Gene Fusion Detection: Rna-Seq Data

Kevin

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written by Kevin Blighe Kevin Blighe

Hi Kevin,

Thank you for your response! I have looked at almost every fusion gene detection tool out there, but unfortunately none supports long read data (like Nanopore) and therefore, I am trying to come up with alternative ideas on how to detect my fusions.

Many thanks,

Peny

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written by pennakiza pennakiza

Hi Kevin,

Thank you for your response! I have looked at almost every fusion gene detection tool out there, but unfortunately none supports long read data (like Nanopore) and therefore, I am trying to come up with alternative ideas on how to detect my fusions.

Many thanks,

Peny

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written by pennakiza pennakiza

Hi pennakiza,

This reply is better suited as a comment on kevin's answer. Could you make the appropriate change please? That would involve the following steps:

  1. Copy the contents of your reply from this answer (you can edit this answer (Ctrl/Cmd + click the link to open it in a new tab) and do a Select All -> Copy there).
  2. Click on Add Comment on Kevin's post here: A: Fusion sequence matching
  3. Paste the copied text
  4. Click on the green Add Comment button
  5. Click on moderate back in your answer here: A: Fusion sequence matching
  6. Choose Delete Post
  7. Click on the blue Submit button.

Thank you!

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written by Ram Ram

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