Hello, I am a new hand and I encountered this problem when I was scaffolding using Juicer with HiC data. The genome size is approximately 680M with ten chromosome. Using the HiC data, I scaffold only 400M to the ten chromosome. Although, many contigs can be scaffolded to the chromosome by eyes, Juicer failed to locate these contigs to the right position. ibb.co/3zCHT8R
I have removed the duplication after canu assembling and the the remaining dups is 2%.
Please help me and thank you so much!