Hi,
I am interested in checking if my genome has telomeric repeats. I see that the program requires various parameters and I wanted to ask if you could suggest me parameters for my genome. I am working with a marine mammal, and my genome assembly now has 176 sequences.
To test TRF I followed the paper: "A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps", and I used their parameters to check for repeats 2 7 7 80 10 500 6 -l 10 -d -h.
I did a first test and I got surprised that the program reported no TR.
I am using the VGP tidk, which is a pain in the ..., and it is detecting them.
Any parameter that I should modify to detect telomere motifs?
Thanks;
Hi,
I am interested in checking if my genome has telomeric repeats. I see that the program requires various parameters and I wanted to ask if you could suggest me parameters for my genome. I am working with a marine mammal, and my genome assembly now has 176 sequences.
To test TRF I followed the paper: "A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps", and I used their parameters to check for repeats 2 7 7 80 10 500 6 -l 10 -d -h.
I did a first test and I got surprised that the program reported no TR.
I am using the VGP tidk, which is a pain in the ..., and it is detecting them.
Any parameter that I should modify to detect telomere motifs?
Thanks;