Hello,
For get high quality SVs, I first aligned the target genome to the ref genome ,then I mapped the ref genome to target genome. I filtered the SVs by intersecting two SVs set and obtained the final SVs. But there was no tandem contraction in either of these comparisons. I think when I do this in reverse, I will get the opposite type of tandem expansion, such as tandem contraction. May I know why
Hello, For get high quality SVs, I first aligned the target genome to the ref genome ,then I mapped the ref genome to target genome. I filtered the SVs by intersecting two SVs set and obtained the final SVs. But there was no tandem contraction in either of these comparisons. I think when I do this in reverse, I will get the opposite type of tandem expansion, such as tandem contraction. May I know why
`minimap2 -ax asm5 --cs -t 10 target_sv.fa ref_sv.fa > Ref2Qry.sam
python ~/Assemblytics/sam2delta.py Ref2Qry.sam
Assemblytics Ref2Qry.sam.delta genome 10000 10 1000000`
Looking forward to your reply, thanks Rilla