For Gene1A (5Gene) the domain retention should not be filtered for only in-frame since the frameshift only affects the Gene1B (3Gene) translation
For example when I was looking at this fusion specifically NEK11--TMEM108 in BS_99B1XRZQ it’s a frameshift fusion and the kinase domain in 5Gene is before the breakpoint . Right now domain retention is “No” because it doesn’t satisfy the “in-frame” condition, but should it be “Yes” if it’s the 5Gene since the frameshift only affects the 3`Gene domain.
Added more comments for the domain retention conditions
For Gene1A (5
Gene) the domain retention should not be filtered for only in-frame since the frameshift only affects the Gene1B (3Gene) translation For example when I was looking at this fusion specifically NEK11--TMEM108 in BS_99B1XRZQ it’s a frameshift fusion and the kinase domain in 5Gene is before the breakpoint . Right now domain retention is “No” because it doesn’t satisfy the “in-frame” condition, but should it be “Yes” if it’s the 5Gene since the frameshift only affects the 3`Gene domain.Added more comments for the domain retention conditions