Gene fusions

[schelhorn]

Hello, are there any plans to also include gene fusion detection in Hisat2, or will that be left to other tools working on the output Samfiles?

[infphilo]

Yes, I plan to implement in HISAT2 fusion alignment and reporting fusions that are strongly supported by reads, similar to TopHat-Fusion. HISAT2's fusion detection will be much faster and more sensible than TopHat-Fusion. Hopefully I will release a working version by spring of next year.

[schelhorn]

Excellent.

[mjafin]

It would be extremely nice if Hisat2 produced "split" reads (besides discordants) so that we could replace STAR in Manta fusion calling for hg38.

[kepbod]

Are there any advances in the implement of HISAT2 fusion alignment? Thanks!

[jrderuiter]

I would also be interested in this!

[schelhorn]

@infphilo could we please reopen this issue? I believe there is sufficient interest for fusion calling and it would really be a great addition to Hisat2. @mjafin, are you guys doing RNA-Seq fusion calling on hg38?

[infphilo]

I reopened this feature request. I know we need a fast and more accurate fusion finding program, and HISAT2 could be a good starting point.

Implementing a fusion calling algorithm may take at least several months (or even more). I won't be able to implement it myself. I'm looking to have my own lab and work with students or postdocs to develop a new method.

[iskandr]

I'm wondering if this ever made progresss

[infphilo]

We're also very interested in developing HISAT-fusion, but we have our hands full with many projects now. Perhaps, one way to help us out is to encourage potential postdocs with strong computational skills to apply for our lab, kim-lab.org.

[Abdubidopsis]

We're also very interested in developing HISAT-fusion, but we have our hands full with many projects now. Perhaps, one way to help us out is to encourage potential postdocs with strong computational skills to apply for our lab, kim-lab.org.

Can anyone write here about Hisat2-fusion?