Interchromosomal misjoin about hifiasm HOT 2 OPEN

Hi,

I did more research on this case, and I realized the interchromosomal misjoin could occurs within the black window. I randomly selected one position within the black window and blat the flanking 10kb sequencing to CHM13. The blat result shows the left 5kb sequence is mapped to chr10, while the right 5kb sequencing is mapped to chrX.

Do you think this is correct way to fix the misjoin issue? Besides, would it possible to avoid such error during assembly?

Thank you!

from hifiasm.

Perhaps the read that was used to build this contig is not begin shown. There should be a read which perfectly matches the assembly. Are you filtering secondary/supplemental alignments in IGV. Are you showing alignments with mapping quality 0?

Another way to troubleshoot is to look into the asm.bp.p_ctg.noseq.gfa file and find the read that used in the tiling path at this location and see why it is not mapping here. I am guessing there bogus or repetitive read that use to create this contig that is not being shown in the visualization.

from hifiasm.