Chromosome Positions in pgd File

[Roxane Dunbar]

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

[Robert Kofler]

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