Sebastian Uhrig

Do you need any further help on this?

Hi, could you kindly pick one read which is aligned by STAR-Fusion but not by Arriba and extract the paired-end reads from the Arriba BAM file using for example `samtools...

Thanks for providing the details. Without any further evidence, I would argue that Arriba is right here. It finds a better alignment than STAR-Fusion. The alignment proposed by Arriba is...

Thanks for your feedback!

I have submitted a PR to the modules repository: https://github.com/nf-core/modules/pull/5024

My PR has been merged into the main branch of nf-core/modules. What is the procedure to get this into the fetchngs pipeline?

Thanks for your guidance. It worked. The PR is ready for review IMO.

To some extent, this is already possible. Technically, Arriba is compatible with STARlong. I just gave it a spin with PacBio long reads and it worked. The `mismappers` filter took...

No time wasted. I will make an enhancement that the `mismappers` filter is skipped for long reads. If you can share any STAR or Arriba parameter optimizations that improve calling,...

In order to detect CIC-DUX4 fusions, it is important to enable multimapping chimeric reads. Did you use `--chimMultimapNmax 50`? If the fusion is not listed in either the fusions.tsv file...