Question: Fusion gene detection in sam file
0
gravatar for pennakiza
10 months ago by
pennakiza20
pennakiza20 wrote:

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

ont nanopore rna-seq fusion • 410 views
ADD COMMENTlink modified 10 months ago by Kevin Blighe41k • written 10 months ago by pennakiza20
0
gravatar for Kevin Blighe
10 months ago by
Kevin Blighe41k
The Ether
Kevin Blighe41k wrote:

They imply that it's possible:

f

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

-------------------------------------

Your best chance is to Contact ONT directly.

Kevin

ADD COMMENTlink modified 10 months ago • written 10 months ago by Kevin Blighe41k

Thank you Kevin,

I have contacted them but no response yet! :(

Peny

ADD REPLYlink written 10 months ago by pennakiza20

Okay, I will contact them right now.

ADD REPLYlink written 10 months ago by Kevin Blighe41k

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."

ADD REPLYlink written 10 months ago by Kevin Blighe41k

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

ADD REPLYlink written 9 months ago by pennakiza20
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