Self mapping for reduce the paralog or TE influence on the local subgraph

[baozg]

Hi, @lh3

I saw some weird subgraphs in A.thaliana with hundreds of long reads genome. AT1G31270 looks normal in the reference annotation, but now we find that it should be an LTR fragment with a new annotation and it lacks support from dozens of long reads RNA-Seq. So this gene mapping position varied between different genomes (different chr, very far location). A.thaliana synteny should be quite good without too many translocations. Is there any way to filter these unreliable mapping?

For species with recent/ancient duplication (fish/flowering plant), miniprot may map these paralogs into different positions. Can we use self-mapping to filter these genes first? If I use the reference annotation map to the reference genome by miniprot, 344 genes cannot find the same chromosomes. However, these genes will break the local subgraph structure.

If you want, I can share you with graph and weird gene list

subgraph1

subgraph2