Adjacent genes classification

[A.R. Grosso]

Which criteria did you use to define fusions between adjacent genes or not? Any threshold distance applied? Or just based on the closest gene search? Did you have in account the strand to define the adjacent genes? P.e. how do you classify if the fusion break is between two genes (both in forward strand) and in the middle there is a gene in the opposite strand (not involved in the fusion)?
Thanks
Ana Rita

[Andrew]

Genes are clustered into sets of overlapping genes. Each gene in a cluster is considered adjacent to each gene in an adjacent cluster. No threshold distance is applied. The strand of genes is not accounted for. As you say, if a small (and maybe insignificant) gene exists between two adjacent fused genes then that fusion will not be classified as between adjacent genes. This is a shortcoming of this particular feature, and one reason I also look at the alt_splice column to identify read throughs.