Entering edit mode
4.2 years ago
O.rka
▴
710
My organism is a novel diatom so the assembly has been de-novo using PacBio reads. I'm getting a large number of reads mapping to more than one location in my genome. I suspect this organism is polyploid so the assembly may have "duplicate" regions. I ran minimap2 using minimap2 -PD -k19 -w19 -m200 -t8 scaffolds.fasta scaffolds.fasta > scaffolds-self.paf as suggested by the author and found large stretches of homology.
How should I proceed? Do I need to somehow dereplicate my polyploid assembly into a (pseudo?)haploid assembly? I've never dealt with this before so any help would be greatly appreciated.
My of my sample replicates do not have a consistent gene overlap because a lot of the reads are being mapped to multiple locations.
