Detecting fusion transcripts in long read or paired-end short read

[cprovido]

In my reading of Fusion-Bloom, it states that paired-RNA seq reads are assembled by RNA-Bloom to reconstruct chimeric transcripts. However, I'm not sure if Fusion-Bloom is still up-to-date.

Is it still possible to generate fusion transcripts from RNA-Bloom or should directly use Fusion-Bloom?

With my second dataset of only long read fastqs from MinION, is chimeric detection supported by RNA-Bloom?

[kmnip]

RNA-Bloom only assembles transcripts from the RNA-seq data, but variant calling is done in PAVFinder (https://github.com/bcgsc/pavfinder). If I remember correctly, PAVFinder only worked with paired-end short reads. We haven't fully tested the code with ONT reads. @readmanchiu can comment on this.