Issues surrounding GenCodev44 reference files

[Ryley Dorney]

Hello team at UCSC,

I have a very niche question,

Is there any major difference in formatting or anything with reference files from GenCodev44?

When using reference files from version 44, JAFFAL will crash and cannot identify fusions (please see this issue on GitHub https://github.com/Oshlack/JAFFA/issues/116). I tested JAFFAL with both GenCodev43 and GenCodev47 and everything runs smoothly. It is only GenCodev44 that crashes JAFFAL.

Instructions on what references files to download and how to download them are here: https://github.com/Oshlack/JAFFA/wiki/FAQandTroubleshooting#how-can-i-generate-the-reference-files-for-a-non-supported-genome

Any pointers or suggestions as to what may be the cause?

Kind regards,

Ryley Dorney 
Please read my book chapter Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events

ResearchGate Profile: https://www.researchgate.net/profile/Ryley-Dorney

Doctor of Philosophy (Medical and Molecular Sciences) Candidate 

Centre for Tropical Bioinformatics and Molecular Biology

Department of Molecular and Cell Biology 

James Cook University, Australia 

Office Hours: Monday to Friday, 9:00am - 5:00pm 

Student Email: ryley....@my.jcu.edu.au | Staff Email: ryley....@jcu.edu.au

JCU Townsville | Bebegu Yumba campus | Building 142 Room 303

1 James Cook Drive Townsville QLD 4811 AUSTRALIA

[Luis Nassar]

Hi, Ryley.

Which specific GENCODE files are you using?

While we host that data, we recommend asking GENCODE directly (https://www.gencodegenes.org/). The fact that it works on 43 and 47 but not on 44 suggests there may be something specific to that release.

Otherwise, we are not familiar with JAFFA, and cannot offer additional assistance.

If you discover that it is something specifically related to our file(s), let us know, and we can dig in further to fix it.

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Lou Nassar
UCSC Genomics Institute