Sebastian Uhrig

Yes, this looks good to me!

What's the transcript that Arriba reports in column `transcript_id2`? Only if the protein sequence is in-frame with respect to this transcript, then Arriba will consider the fusion protein to be...

I have taken a close look at this case. The reason why Arriba chooses the intron retention transcript is because there is some intron retention going on. Namely, the bases...

Apologies for the long delay and also for the fact that I still have not come up with a solution yet despite the long time. However, your provided data was...

Thanks for the hint, @sermare. In the meantime, I have implemented an enhancement for the selection of transcripts. Arriba now has a preference for transcripts with a long coding sequence....

Hi Thomas, This is not possible at the moment. Good suggestion, though, and not too hard to implement. I'm contemplating whether it makes more sense to have an option to...

Probably too late for you, but I finally found the time to implement a new parameter `--plotPanels`, which can be used to omit panels from the figure. The default value...

Apologies for the delay. The default parameters for Arriba and the customized parameters for STAR are what is recommended for most scenarios. I try to make the tool as straightforward...

> but of note for certain data's, arriba shows less fusion support than Starfusion. This could be because Arriba only counts high-quality alignments in the columns `split_reads1/2` and `discordant_mates`. There...

> When I zip the Homo_sapiens.GRCh38.dna.primary_assembly.fa What command did you use to compress the file? You must use `gzip` for this, not `zip`. > EXITING because of INPUT ERROR: the...