We generated a (diploid, chordata, highly heterozgous) genome using PacBio and we wanted to see whether it contains lineage-specific duplications (paralogs, basically). The genome is not in Ensembl yet.
The only data we have at the moment are:
- transcript annotation
We found some methods from papers:
- use Blast
- detect segmental duplications in complete genomes with SDDdetector
- detecting putative recent segmental duplications or diploid homozygous organisms based on NGS data DuplicationDetector
- (I just came up with this, but should work) map back the reads to the assembly & analyze the read depth to detect duplicated portions
I'll gladly take advice.