zhangrengang

I have the same issue when runing augustus v3.4.

About 1M bp.

In total, two issues of this type are observed in my assembly: one is ~1 Mbp (the above) and the other is ~400 Kbp. The 400kb is somewhat different as...

No. I combine hap1 and hap2 in HiC heatmap, so it will be present in the heatmap if it is in either haps.

I am sorry that the data is not my own, so I can not share.

Thanks. I have tried and the missed unitig is present this time.

It should be an unexpected breakpoint, as it is connected on the unitig graph and neighboured on the Hi-C heatmap.

The breakpoint is absent with another HiC dataset by a different enzyme.

Yes, but it is limited by the databases. For rexdb, LTR-RTs are not well classified like those of plants.

The gene family counts is separated by TAB.