Hi,

We're trying to call fusion transcripts in cervical cancers with HPV, using a reference we created by adding various HPV strains to hg38. When we run LongGF on data aligned to this reference, using a combined hg38/HPV gtf file, it calls fusions between human genes, but ignores the HPV-containing reads. (We can definitely see fusion reads between the HPV and hg38 genes when we look in IGV).

The HPV "chromosomes" all have names like "HPV16", "HPV18", etc. Does LongGF ignore genes on chromosomes that don't start with the string "chr"? If so, how could we override that behaviour?

Thanks!