This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Fusion gene detection in sam file

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

rna-seq fusion nanopore ont
• 2,439 views • link
updated by Kevin Blighe Kevin Blighe • written by pennakiza pennakiza

1 answer

They imply that it's possible:

f

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

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

Your best chance is to Contact ONT directly.

Kevin

• 1 views • link
written by Kevin Blighe Kevin Blighe

Thank you Kevin,

I have contacted them but no response yet! :(

Peny

• 1 views • link
written by pennakiza pennakiza

Okay, I will contact them right now.

• 1 views • link
written by Kevin Blighe Kevin Blighe

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

• 1 views • link
written by pennakiza pennakiza

Log in to answer this question.

More posts like this