Simulate genomes with different proportions of TEs

Robert Kofler — Fri, 24 Jan 2020 10:26:08 -0000

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

Simulate genomes with different proportions of TEs

Solomon Chak — Thu, 19 Sep 2019 01:40:15 -0000

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

chassis

Solomon Chak — Thu, 19 Sep 2019 01:39:51 -0000

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

Chromosome Positions in pgd File

Robert Kofler — Tue, 26 Feb 2019 21:04:49 -0000

Hi Roxane,

unfortunatelly SimulaTE does not support multiple chromosomes. Mostly because i did not think it is necessary when simulating TE landscapes. Simulated landscapes are mostly used for evaluating different tools where chromosomes are usually not important. So my first question would be: are you absolutly sure you need multiple chromsomes?
In case you absolutely do need them the only way I can think of is concatenating the sequences of your chromosomes and maybe enter a easily recognizable sequence in between eg AGAGAGAGAGAGAGAGAGAGAG or NNNNNNNNNNNNN this can than later be used to split them again.

cheers and sorry for the unpleasant news,
ro

Chromosome Positions in pgd File

Roxane Dunbar — Sun, 24 Feb 2019 21:36:22 -0000

Hi,

Does SimulaTE recognise chromosome positions in the pgd file? E.g:

Chasis hs37d5; Length 2867688499 nt

1=$1 # L19088.1 Human LINE1 (L1.3) repetitive element DNA sequence
chr1:1327571 1-
chr2:3743706 1+
chr3:17103970 * *

If not, how could one go about creating a pdg file for a whole genome containing multiple chromosomes?

Kindest regards,
Roxane

Recent posts to Discussion

Simulate genomes with different proportions of TEs

Simulate genomes with different proportions of TEs

chassis

Chromosome Positions in pgd File

Chromosome Positions in pgd File

Chasis hs37d5; Length 2867688499 nt