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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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Gene fusions #8

Open schelhorn opened 8 years ago

schelhorn commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

Excellent.

mjafin commented 8 years ago

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 commented 8 years ago

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

jrderuiter commented 8 years ago

I would also be interested in this!

schelhorn commented 7 years ago

@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 commented 7 years ago

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 commented 6 years ago

I'm wondering if this ever made progresss

infphilo commented 6 years ago

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 commented 5 years ago

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?