Simulate genomes with different proportions of TEs

[Solomon Chak]

Hi, I want to simulate genomes with different proportions of TEs, say, based on the human genome. Will SimulaTE be able to do that?

[Robert Kofler]

Hi Solomon,
sorry for the late response, I only found your comment just now.
You can provide a pgd-file that mirrors the proportion of TEs in the human genome. But this pgd file needs to be generated manually. You can not just enter proportions, you need to specify the insertion sites of each TE. But you could write a script that translates the proportions into a pgd files with random insertions sites for example.
cheers ro