suhrig

Your added line looks good to me. Just make sure that it is tab-separated (Arriba should print a warning if that's not the case). Fusions listed in the know fusions...

Dear Elmer, > You said: "Fusions listed in the know fusions file will only be recovered if they are supported by at least two reads." > But where is this...

> Up to now I am failing in adding new know fusions to recover. Hm, if Arriba does not complain about your manually added lines, then they should be syntactically...

I did some further tests with the known fusions filter. I found a minor bug: It did not complain when mandatory columns were empty and just silently ignored the affected...

On second thought, it may be best to send me the BAMs. This way, I will save the effort to do the alignment, and - more importantly - there is...

Hi @elmerfer, Do you still plan on sending the BAM file(s)? Or is this issue no longer relevant? Kind regards, Sebastian

I can send you the commands to build your own STAR index, but I need to know the following details: - Which annotation (GTF) did you download? - Which assembly...

It seems like you have already done most of the work! Since you already have adapted the variables `ASSEMBLY` and `ANNOTATINON`, all that is left to do is to remove...

Please refer to the [manual](https://arriba.readthedocs.io/en/latest/quickstart/#manual-installation) on how to use `download_references.sh`. Notably, you should not call the script with `sh`. It's not an `sh` script, it is a `bash` script. The...

> How Can I extract the reads that support two genes' fusion. There is a script for exactly this propose: https://github.com/suhrig/arriba/blob/master/scripts/extract_fusion-supporting_alignments.sh Run it without arguments to learn about it's usage....