Sven-Eric Schelhorn

Update: in the meantime, this dirty patch allows reading in the allele-specific files as described above (no guarantees, though ;): ```R checkDataTypeInput2

Excellent. May I point out that tools such as Oncofuse https://github.com/mikessh/oncofuse/ and Pegasus https://github.com/RabadanLab/Pegasus have a particular, additional value since they provide functional annotation of fusion events identified by other...

Hello @rob-p, may I ask whether there are any news concerning gene fusion detection in Salmon?

Great; would you like help testing the pipeline, and integrating it into bcbio? We could help with both :)

Also, do you know if the Salmon pseudo-BAM is suitable for fusion calling by standard (alignment-based) fusion calling tools, ie does the BAM include information on mate pairs mapped across...

Excellent; thank you. We'll have a look and see what we can contribute.

Hello @rob-p, could you please invite @tetianakh to the repo as well? She'll do the development on our end. Thanks!

Sweet!

FYI, I also asked in the kallisto project: https://github.com/pachterlab/kallisto/issues/122

Great; directly in the repo is preferred.