Fusion gene detection in sam file

Question

[pennakiza]

Hello all,

I am using Oxford Nanopore direct cDNA sequencing data and I have aligned them with GraphMap. I am looking for fusions and I would like to do that by using my sam files. Unfortunately, I haven't managed to find any tools to use, as none of them is compatible with ONT data. Any suggestions would actually save my life right now! :)

Many thanks,

Peny

Answer 1

[Kevin Blighe]

They imply that it's possible:

[source: https://nanoporetech.com/transcriptomics]

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Your best chance is to Contact ONT directly.

Kevin

[pennakiza]

Thank you Kevin,

I have contacted them but no response yet! :(

Peny

[Kevin Blighe]

Okay, I will contact them right now.

[Kevin Blighe]

They directed me to this video: https://nanoporetech.com/resource-centre/talk/clinical-applications-real-time-sequencing-leukaemia

However, they stated that they do not have a "specific pipeline for fusion gene discovery."

[pennakiza]

Hi Kevin,

They said the same to me but in my opinion the pipeline presented in this video is not very clear. They have suggested Sniffles, Picky and NanoSV (which actually works) but these tools give me only Structural Variations - I guess users have to decide which of them are fusions and whether they are important or not. To be honest this is not very convinient for our project!

Best

Peny