salzmanlab-admin / deepest-fusion Goto Github PK

Dear authors, we would like to run Deepest on our own dataset of 1000 tumor samples. We wonder whether the different cohort size will affect the expectation statistics and thus could lead to a significantly different call sensitivity than in your TCGA study. What would be the best overall strategy if we want to compare fusion calls between TCGA and our own cohort?
All the best,
Daniel

Is there a known_fusions.fa for hg19 available, or a guide for how to create one? Since I am working with hg19 I am following the README to create my own reference files. I have the reference genome fasta and annotation gtf, but not a list of known fusions.

The README simply says that the known fusions fasta is "a list of known fusions constructed based on ChimerDB 3.0 curated list of known cancer fusions", but doesn't specify how this is done.