Custom references for JAFFAL !!!

[KM belal hossain monju1]

Hello Nadia,

I've analyzed the simulated demo data using JAFFAL and the program successfully detected the fusion transcript. 

Now I want to use JAFFAL to analyze Nanopore data to identify virus-host chimeric transcript. But the issue is the references. I've the .gtf format of the custom reference where the virus sequence was added as a separate chromosome. 

Is it okay to use this as a reference??

If okay, maybe to run JAFFAL, I need the .tab, .fasta and .BED format of the custom reference, can you help me if I could convert .gtf to .tab/.fasta/.BED format.

Thanking you,

Belal

[Nadia Davidson]

Hello Belal,

Sorry for the VERY slow reply. This sounds like a great application of fusion calling. We don't have any automated way to create the reference files for virus, but if you have any questions about how they can be constructed manually I'm happy to advise.

All the best,

Nadia.