Comments (2)
suhrig
commented on July 23, 2024
Hi, can you send me links to the various reference files that you mention so I can better understand the differences between them? Thanks!
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suhrig
commented on July 23, 2024
Hi, I'm closing this issue due to lack of feedback.
In general, it is possible to use any GTF annotation you wish - as long as its coordinates are compatible with the assemblies supported by Arriba (GRCh37, GRCh38). In my experience, GENCODE annotation works best, since it has the most comprehensive annotation. And using a newer version (V43) should be perfectly fine. So if your Ribo-seq experiment used V43, feel free to pass the same GTF file to Arriba. There will be slight differences in the fusion calls, but they should not be substantial and should mostly affect low-confidence fusions.
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